From noreply ＠ sourceforge.jp Wed Nov 7 18:56:08 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 07 Nov 2012 18:56:08 +0900 Subject: [Molds-dev] [molds] #30041: Set a lower limit to a trust radius Message-ID: <1352282168.364278.9950.nullmailer@sourceforge.jp> #30041: Set a lower limit to a trust radius Open Date: 2012-11-07 18:56 Last Update: 2012-11-07 18:56 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30041 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30041 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-07 18:56 Update by: ktns * New Ticket "Set a lower limit to a trust radius" created --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: バグ Status: オープン Priority: 5 - 中 MileStone: (未割り当て) Component: (未割り当て) Severity: 6 Resolution: なし --------------------------------------------------------------------- Ticket details: In optimization process employing the BFGS method, if an approximate Hessian matrix is poor, a trust radius goes smaller and smaller as an optimization process proceeds. And if an approximate Hessian is too poor, a trust radius goes too small and it seems to lead the calculation to the numerically unstable situation. By setting a lower limit to a trust radius, I think this problem can be avoided. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30041 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30041 From noreply ＠ sourceforge.jp Wed Nov 7 23:35:25 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 07 Nov 2012 23:35:25 +0900 Subject: [Molds-dev] [molds] #30044: Overloaded constructor of MolDSException for boost::format Message-ID: <1352298925.600610.21228.nullmailer@sourceforge.jp> #30044: Overloaded constructor of MolDSException for boost::format Open Date: 2012-11-07 23:35 Last Update: 2012-11-07 23:35 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30044 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30044 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-07 23:35 Update by: ktns * New Ticket "Overloaded constructor of MolDSException for boost::format" created --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: パッチ Status: オープン Priority: 3 MileStone: (未割り当て) Component: (未割り当て) Severity: 3 Resolution: なし --------------------------------------------------------------------- Ticket details: {{{ code cpp throw MolDSException(boost::format("%s: %d\n") % str % num); }}} -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30044 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30044 From noreply ＠ sourceforge.jp Thu Nov 8 03:45:16 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 08 Nov 2012 03:45:16 +0900 Subject: [Molds-dev] [molds] #30045: GetForce returns NaN Message-ID: <1352313916.705218.14130.nullmailer@sourceforge.jp> #30045: GetForce returns NaN Open Date: 2012-11-08 03:45 Last Update: 2012-11-08 03:45 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30045 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30045 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-08 03:45 Update by: ktns * New Ticket "GetForce returns NaN" created --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: (未割り当て) Type: バグ Status: オープン Priority: 7 MileStone: (未割り当て) Component: (未割り当て) Severity: 7 Resolution: なし --------------------------------------------------------------------- Ticket details: If a geometry has two atoms which x and y coordinates are exactly same, GetForce returns a vector that contains NaN. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30045 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30045 From noreply ＠ sourceforge.jp Thu Nov 8 03:52:15 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 08 Nov 2012 03:52:15 +0900 Subject: [Molds-dev] [molds] #30045: GetForce returns NaN Message-ID: <1352314335.859493.23031.nullmailer@sourceforge.jp> #30045: GetForce returns NaN Open Date: 2012-11-08 03:45 Last Update: 2012-11-08 03:52 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30045 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30045 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-08 03:52 Update by: ktns Comment: This bug is found in r1105 --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: (未割り当て) Type: バグ Status: オープン Priority: 7 MileStone: (未割り当て) Component: (未割り当て) Severity: 7 Resolution: なし --------------------------------------------------------------------- Ticket details: If a geometry has two atoms which x and y coordinates are exactly same, GetForce returns a vector that contains NaN. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30045 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30045 From noreply ＠ sourceforge.jp Thu Nov 8 10:31:32 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 08 Nov 2012 10:31:32 +0900 Subject: [Molds-dev] [molds] #30045: GetForce returns NaN Message-ID: <1352338292.462384.11994.nullmailer@sourceforge.jp> #30045: GetForce returns NaN Open Date: 2012-11-08 03:45 Last Update: 2012-11-08 10:31 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30045 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30045 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-08 10:31 Update by: mikiya_fujii Comment: I found a "theoretical" bug which causes this NaN in r1105. The variable "double r" in the Cndo2::CalcRotatingMatrix1stDerivatives is 0 when x=y=0, which leads to 0-divide. The variable "double r" in the Cndo2::CalcRotatingMatrix2ndDerivatives causes same error. To fix these bugs, re-fomulation of the 1st and 2nd derivatives of rotating matrix is needed --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: (未割り当て) Type: バグ Status: オープン Priority: 7 MileStone: (未割り当て) Component: (未割り当て) Severity: 7 Resolution: なし --------------------------------------------------------------------- Ticket details: If a geometry has two atoms which x and y coordinates are exactly same, GetForce returns a vector that contains NaN. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30045 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30045 From okymmolds ＠ gmail.com Thu Nov 8 11:17:21 2012 From: okymmolds ＠ gmail.com (okymmolds) Date: Thu, 8 Nov 2012 11:17:21 +0900 Subject: [Molds-dev] Unpaired_electron_population_code Message-ID: <20121108111721.6e527055.okymmolds@gmail.com> Dear Fujii A patch file to calculate unpaired electron population on ground state has been developed, where it's impossible to calculate the population of excited states. orz I send this patch file to you. I wold like to get some opinion from you. Best regards. M.Okuyama ------- How to patch by this patch file: In revision 1106 source code, you can introduce a calculation of unpaired electron population to your MolDS by the following command, mv unapired_pop.patch (work directory)/trunk/src cd trunk/src patch -p0 < unpaired_pop.patch --------- About output of unpaired electron population: For example, in src directory, if you execute the following command, ./MolDS.out ../test/h2o_zindos_directCIS_singlet.in, you can find the following output, | i-th | atom type | Unpaired electron population[a.u.]| Unpaired electron population: 0 O 2.220446e-15 Unpaired electron population: 1 H 0.000000e+00 Unpaired electron population: 2 H -1.110223e-15 . This is the output of unpaired electron population. I will send this log as 'h2o_zindos_directCIS_singlet.log'. The above case is an example. In the job that calculates Mulliken charge, the calculation of the unpaired electron population is executed. -- okymmolds From mikiya.fujii ＠ gmail.com Thu Nov 8 12:35:30 2012 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Thu, 8 Nov 2012 12:35:30 +0900 Subject: [Molds-dev] Unpaired_electron_population_code In-Reply-To: <20121108111721.6e527055.okymmolds@gmail.com> References: <20121108111721.6e527055.okymmolds@gmail.com> Message-ID: Dear M.Okuyama, Thanks for your contributions!!! However, the attached files were discarded by the mailing-list-system. I modified the setting of the mailing-list-system to allow attached files. Thus, please send the mail with the attached files again. My best, Mikiya *************************************** Mikiya Fujii, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: fujii ＠ tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** 2012/11/8 okymmolds : > > Dear Fujii > > A patch file to calculate unpaired electron population > on ground state has been developed, where it's impossible to calculate > the population of excited states. orz > I send this patch file to you. > I wold like to get some opinion from you. > > Best regards. > > M.Okuyama > > ------- > How to patch by this patch file: > > In revision 1106 source code, you can introduce > a calculation of unpaired electron population to > your MolDS by the following command, > > mv unapired_pop.patch (work directory)/trunk/src > cd trunk/src > patch -p0 < unpaired_pop.patch > > --------- > About output of unpaired electron population: > For example, in src directory, if you execute the following command, > > ./MolDS.out ../test/h2o_zindos_directCIS_singlet.in, > > you can find the following output, > > | i-th | atom type | Unpaired electron population[a.u.]| > Unpaired electron population: 0 O 2.220446e-15 > Unpaired electron population: 1 H 0.000000e+00 > Unpaired electron population: 2 H -1.110223e-15 > > . This is the output of unpaired electron population. > I will send this log as 'h2o_zindos_directCIS_singlet.log'. > > The above case is an example. > In the job that calculates Mulliken charge, the calculation > of the unpaired electron population is executed. > > -- > okymmolds > _______________________________________________ > MolDS-dev mailing list > MolDS-dev ＠ lists.sourceforge.jp > http://lists.sourceforge.jp/mailman/listinfo/molds-dev From okymmolds ＠ gmail.com Thu Nov 8 12:49:47 2012 From: okymmolds ＠ gmail.com (okymmolds) Date: Thu, 8 Nov 2012 12:49:47 +0900 Subject: [Molds-dev] Unpaired_electron_population_code In-Reply-To: References: <20121108111721.6e527055.okymmolds@gmail.com> Message-ID: <20121108124947.e76d6a86.okymmolds@gmail.com> Dear Mr. Fujii I understood the following contents of the E-mail that you send to me. I will send the files to you again. Best regards. M.Okuyama. On Thu, 8 Nov 2012 12:35:30 +0900 Mikiya Fujii wrote: > Dear M.Okuyama, > > Thanks for your contributions!!! > However, the attached files were discarded by the mailing-list-system. > > I modified the setting of the mailing-list-system to allow attached files. > Thus, please send the mail with the attached files again. > > My best, > Mikiya > > > > > > > *************************************** > Mikiya Fujii, Ph.D. > > Yamashita & Ushiyama Laboratory, > Department of Chemical System Engineering, > Faculty of Engineering, > The University of Tokyo. > > tel&fax: +81-3-5841-7286 > email: fujii ＠ tcl.t.u-tokyo.ac.jp > HP: http://www.tcl.t.u-tokyo.ac.jp/ > *************************************** > > > 2012/11/8 okymmolds : > > > > Dear Fujii > > > > A patch file to calculate unpaired electron population > > on ground state has been developed, where it's impossible to calculate > > the population of excited states. orz > > I send this patch file to you. > > I wold like to get some opinion from you. > > > > Best regards. > > > > M.Okuyama > > > > ------- > > How to patch by this patch file: > > > > In revision 1106 source code, you can introduce > > a calculation of unpaired electron population to > > your MolDS by the following command, > > > > mv unapired_pop.patch (work directory)/trunk/src > > cd trunk/src > > patch -p0 < unpaired_pop.patch > > > > --------- > > About output of unpaired electron population: > > For example, in src directory, if you execute the following command, > > > > ./MolDS.out ../test/h2o_zindos_directCIS_singlet.in, > > > > you can find the following output, > > > > | i-th | atom type | Unpaired electron population[a.u.]| > > Unpaired electron population: 0 O 2.220446e-15 > > Unpaired electron population: 1 H 0.000000e+00 > > Unpaired electron population: 2 H -1.110223e-15 > > > > . This is the output of unpaired electron population. > > I will send this log as 'h2o_zindos_directCIS_singlet.log'. > > > > The above case is an example. > > In the job that calculates Mulliken charge, the calculation > > of the unpaired electron population is executed. > > > > -- > > okymmolds > > _______________________________________________ > > MolDS-dev mailing list > > MolDS-dev ＠ lists.sourceforge.jp > > http://lists.sourceforge.jp/mailman/listinfo/molds-dev > > _______________________________________________ > MolDS-dev mailing list > MolDS-dev ＠ lists.sourceforge.jp > http://lists.sourceforge.jp/mailman/listinfo/molds-dev -- okymmolds -------------- next part -------------- テキスト形式以外の添付ファイルを保管しました... ファイル名: unpaired_pop.patch 型: text/x-diff サイズ: 7815 バイト 説明: 無し URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20121108/7918412a/attachment.patch -------------- next part -------------- テキスト形式以外の添付ファイルを保管しました... ファイル名: h2o_zindos_directCIS_singlet.log 型: application/octet-stream サイズ: 9734 バイト 説明: 無し URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20121108/7918412a/attachment.obj From okymmolds ＠ gmail.com Thu Nov 8 12:53:32 2012 From: okymmolds ＠ gmail.com (okymmolds) Date: Thu, 8 Nov 2012 12:53:32 +0900 Subject: [Molds-dev] Unpaired_electron_population_code In-Reply-To: References: <20121108111721.6e527055.okymmolds@gmail.com> Message-ID: <20121108125332.f37fca9f.okymmolds@gmail.com> Dear Mr. Fujii I understood the following contents of the E-mail that you send to me. I will send the files to you again. Best regards. M.Okuyama. On Thu, 8 Nov 2012 12:35:30 +0900 Mikiya Fujii wrote: > Dear M.Okuyama, > > Thanks for your contributions!!! > However, the attached files were discarded by the mailing-list-system. > > I modified the setting of the mailing-list-system to allow attached files. > Thus, please send the mail with the attached files again. > > My best, > Mikiya > > > > > > > *************************************** > Mikiya Fujii, Ph.D. > > Yamashita & Ushiyama Laboratory, > Department of Chemical System Engineering, > Faculty of Engineering, > The University of Tokyo. > > tel&fax: +81-3-5841-7286 > email: fujii ＠ tcl.t.u-tokyo.ac.jp > HP: http://www.tcl.t.u-tokyo.ac.jp/ > *************************************** > > > 2012/11/8 okymmolds : > > > > Dear Fujii > > > > A patch file to calculate unpaired electron population > > on ground state has been developed, where it's impossible to calculate > > the population of excited states. orz > > I send this patch file to you. > > I wold like to get some opinion from you. > > > > Best regards. > > > > M.Okuyama > > > > ------- > > How to patch by this patch file: > > > > In revision 1106 source code, you can introduce > > a calculation of unpaired electron population to > > your MolDS by the following command, > > > > mv unapired_pop.patch (work directory)/trunk/src > > cd trunk/src > > patch -p0 < unpaired_pop.patch > > > > --------- > > About output of unpaired electron population: > > For example, in src directory, if you execute the following command, > > > > ./MolDS.out ../test/h2o_zindos_directCIS_singlet.in, > > > > you can find the following output, > > > > | i-th | atom type | Unpaired electron population[a.u.]| > > Unpaired electron population: 0 O 2.220446e-15 > > Unpaired electron population: 1 H 0.000000e+00 > > Unpaired electron population: 2 H -1.110223e-15 > > > > . This is the output of unpaired electron population. > > I will send this log as 'h2o_zindos_directCIS_singlet.log'. > > > > The above case is an example. > > In the job that calculates Mulliken charge, the calculation > > of the unpaired electron population is executed. > > > > -- > > okymmolds > > _______________________________________________ > > MolDS-dev mailing list > > MolDS-dev ＠ lists.sourceforge.jp > > http://lists.sourceforge.jp/mailman/listinfo/molds-dev > > _______________________________________________ > MolDS-dev mailing list > MolDS-dev ＠ lists.sourceforge.jp > http://lists.sourceforge.jp/mailman/listinfo/molds-dev -- okymmolds -------------- next part -------------- テキスト形式以外の添付ファイルを保管しました... ファイル名: unpaired_pop.patch 型: text/x-diff サイズ: 7815 バイト 説明: 無し URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20121108/7acd1a1f/attachment.patch -------------- next part -------------- テキスト形式以外の添付ファイルを保管しました... ファイル名: h2o_zindos_directCIS_singlet.log 型: application/octet-stream サイズ: 9734 バイト 説明: 無し URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20121108/7acd1a1f/attachment.obj From okymmolds ＠ gmail.com Fri Nov 9 09:20:37 2012 From: okymmolds ＠ gmail.com (Okuyama) Date: Fri, 09 Nov 2012 09:20:37 +0900 Subject: [Molds-dev] Unpaired_electron_population_code In-Reply-To: References: <20121108111721.6e527055.okymmolds@gmail.com> Message-ID: <509C4C55.3010706@gmail.com> Dear Mr. Fujii After receiving the mail of the following contents, I send the mail with attached files again to Molds-dev mailing list. Could you receive my mail ? Best regards. M. Okuyama (2012年11月08日 12:35), Mikiya Fujii wrote: > Dear M.Okuyama, > > Thanks for your contributions!!! > However, the attached files were discarded by the mailing-list-system. > > I modified the setting of the mailing-list-system to allow attached files. > Thus, please send the mail with the attached files again. > > My best, > Mikiya > > > > > > > *************************************** > Mikiya Fujii, Ph.D. > > Yamashita & Ushiyama Laboratory, > Department of Chemical System Engineering, > Faculty of Engineering, > The University of Tokyo. > > tel&fax: +81-3-5841-7286 > email: fujii ＠ tcl.t.u-tokyo.ac.jp > HP: http://www.tcl.t.u-tokyo.ac.jp/ > *************************************** > > > 2012/11/8 okymmolds : >> >> Dear Fujii >> >> A patch file to calculate unpaired electron population >> on ground state has been developed, where it's impossible to calculate >> the population of excited states. orz >> I send this patch file to you. >> I wold like to get some opinion from you. >> >> Best regards. >> >> M.Okuyama >> >> ------- >> How to patch by this patch file: >> >> In revision 1106 source code, you can introduce >> a calculation of unpaired electron population to >> your MolDS by the following command, >> >> mv unapired_pop.patch (work directory)/trunk/src >> cd trunk/src >> patch -p0 < unpaired_pop.patch >> >> --------- >> About output of unpaired electron population: >> For example, in src directory, if you execute the following command, >> >> ./MolDS.out ../test/h2o_zindos_directCIS_singlet.in, >> >> you can find the following output, >> >> | i-th | atom type | Unpaired electron population[a.u.]| >> Unpaired electron population: 0 O 2.220446e-15 >> Unpaired electron population: 1 H 0.000000e+00 >> Unpaired electron population: 2 H -1.110223e-15 >> >> . This is the output of unpaired electron population. >> I will send this log as 'h2o_zindos_directCIS_singlet.log'. >> >> The above case is an example. >> In the job that calculates Mulliken charge, the calculation >> of the unpaired electron population is executed. >> >> -- >> okymmolds >> _______________________________________________ >> MolDS-dev mailing list >> MolDS-dev ＠ lists.sourceforge.jp >> http://lists.sourceforge.jp/mailman/listinfo/molds-dev > > _______________________________________________ > MolDS-dev mailing list > MolDS-dev ＠ lists.sourceforge.jp > http://lists.sourceforge.jp/mailman/listinfo/molds-dev > -- ------------------------- Michihiro Okuyama okymmolds ＠ gmail.com ------------------------- From mikiya.fujii ＠ gmail.com Fri Nov 9 09:25:42 2012 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Fri, 9 Nov 2012 09:25:42 +0900 Subject: [Molds-dev] Unpaired_electron_population_code In-Reply-To: <509C4C55.3010706@gmail.com> References: <20121108111721.6e527055.okymmolds@gmail.com> <509C4C55.3010706@gmail.com> Message-ID: Dear Michihiro, I received the mail with the attached files. Sorry, I could not check your coding yesterday. But I am checking your code just now! Please wait a moment. Anyway, are you in holiday? Best, Mikiya *************************************** Mikiya Fujii, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: fujii ＠ tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** 2012/11/9 Okuyama : > > Dear Mr. Fujii > > After receiving the mail of the following contents, > I send the mail with attached files again to Molds-dev mailing list. > Could you receive my mail ? > > Best regards. > > M. Okuyama > > (2012年11月08日 12:35), Mikiya Fujii wrote: >> Dear M.Okuyama, >> >> Thanks for your contributions!!! >> However, the attached files were discarded by the mailing-list-system. >> >> I modified the setting of the mailing-list-system to allow attached files. >> Thus, please send the mail with the attached files again. >> >> My best, >> Mikiya >> >> >> >> >> >> >> *************************************** >> Mikiya Fujii, Ph.D. >> >> Yamashita & Ushiyama Laboratory, >> Department of Chemical System Engineering, >> Faculty of Engineering, >> The University of Tokyo. >> >> tel&fax: +81-3-5841-7286 >> email: fujii ＠ tcl.t.u-tokyo.ac.jp >> HP: http://www.tcl.t.u-tokyo.ac.jp/ >> *************************************** >> >> >> 2012/11/8 okymmolds : >>> >>> Dear Fujii >>> >>> A patch file to calculate unpaired electron population >>> on ground state has been developed, where it's impossible to calculate >>> the population of excited states. orz >>> I send this patch file to you. >>> I wold like to get some opinion from you. >>> >>> Best regards. >>> >>> M.Okuyama >>> >>> ------- >>> How to patch by this patch file: >>> >>> In revision 1106 source code, you can introduce >>> a calculation of unpaired electron population to >>> your MolDS by the following command, >>> >>> mv unapired_pop.patch (work directory)/trunk/src >>> cd trunk/src >>> patch -p0 < unpaired_pop.patch >>> >>> --------- >>> About output of unpaired electron population: >>> For example, in src directory, if you execute the following command, >>> >>> ./MolDS.out ../test/h2o_zindos_directCIS_singlet.in, >>> >>> you can find the following output, >>> >>> | i-th | atom type | Unpaired electron population[a.u.]| >>> Unpaired electron population: 0 O 2.220446e-15 >>> Unpaired electron population: 1 H 0.000000e+00 >>> Unpaired electron population: 2 H -1.110223e-15 >>> >>> . This is the output of unpaired electron population. >>> I will send this log as 'h2o_zindos_directCIS_singlet.log'. >>> >>> The above case is an example. >>> In the job that calculates Mulliken charge, the calculation >>> of the unpaired electron population is executed. >>> >>> -- >>> okymmolds >>> _______________________________________________ >>> MolDS-dev mailing list >>> MolDS-dev ＠ lists.sourceforge.jp >>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >> >> _______________________________________________ >> MolDS-dev mailing list >> MolDS-dev ＠ lists.sourceforge.jp >> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >> > > > -- > ------------------------- > Michihiro Okuyama > okymmolds ＠ gmail.com > ------------------------- > > _______________________________________________ > MolDS-dev mailing list > MolDS-dev ＠ lists.sourceforge.jp > http://lists.sourceforge.jp/mailman/listinfo/molds-dev From okymmolds ＠ gmail.com Fri Nov 9 09:43:24 2012 From: okymmolds ＠ gmail.com (okuyama) Date: Fri, 09 Nov 2012 09:43:24 +0900 Subject: [Molds-dev] Unpaired_electron_population_code In-Reply-To: References: <20121108111721.6e527055.okymmolds@gmail.com> <509C4C55.3010706@gmail.com> Message-ID: <509C51AC.7060406@gmail.com> Dear Mr. Fujii Thanks for your E-mail. O.K. I thought that I'd like to confirm whether I could send the mail or not. That's becauseI start using a new e-mailer. I'min holiday since last Saturday. I'm going to start my job from next Monday. So, I can take enough time to developthe Molds until it. I'm going to take abreakfast now. Best regards. M.Okuyama (2012/11/09 9:25), Mikiya Fujii wrote: > Dear Michihiro, > > I received the mail with the attached files. > Sorry, I could not check your coding yesterday. > > But I am checking your code just now! > Please wait a moment. > > Anyway, are you in holiday? > > Best, > Mikiya > > > > *************************************** > Mikiya Fujii, Ph.D. > > Yamashita & Ushiyama Laboratory, > Department of Chemical System Engineering, > Faculty of Engineering, > The University of Tokyo. > > tel&fax: +81-3-5841-7286 > email: fujii ＠ tcl.t.u-tokyo.ac.jp > HP: http://www.tcl.t.u-tokyo.ac.jp/ > *************************************** > > > 2012/11/9 Okuyama : >> Dear Mr. Fujii >> >> After receiving the mail of the following contents, >> I send the mail with attached files again to Molds-dev mailing list. >> Could you receive my mail ? >> >> Best regards. >> >> M. Okuyama >> >> (2012年11月08日 12:35), Mikiya Fujii wrote: >>> Dear M.Okuyama, >>> >>> Thanks for your contributions!!! >>> However, the attached files were discarded by the mailing-list-system. >>> >>> I modified the setting of the mailing-list-system to allow attached files. >>> Thus, please send the mail with the attached files again. >>> >>> My best, >>> Mikiya >>> >>> >>> >>> >>> >>> >>> *************************************** >>> Mikiya Fujii, Ph.D. >>> >>> Yamashita & Ushiyama Laboratory, >>> Department of Chemical System Engineering, >>> Faculty of Engineering, >>> The University of Tokyo. >>> >>> tel&fax: +81-3-5841-7286 >>> email: fujii ＠ tcl.t.u-tokyo.ac.jp >>> HP: http://www.tcl.t.u-tokyo.ac.jp/ >>> *************************************** >>> >>> >>> 2012/11/8 okymmolds : >>>> Dear Fujii >>>> >>>> A patch file to calculate unpaired electron population >>>> on ground state has been developed, where it's impossible to calculate >>>> the population of excited states. orz >>>> I send this patch file to you. >>>> I wold like to get some opinion from you. >>>> >>>> Best regards. >>>> >>>> M.Okuyama >>>> >>>> ------- >>>> How to patch by this patch file: >>>> >>>> In revision 1106 source code, you can introduce >>>> a calculation of unpaired electron population to >>>> your MolDS by the following command, >>>> >>>> mv unapired_pop.patch (work directory)/trunk/src >>>> cd trunk/src >>>> patch -p0 < unpaired_pop.patch >>>> >>>> --------- >>>> About output of unpaired electron population: >>>> For example, in src directory, if you execute the following command, >>>> >>>> ./MolDS.out ../test/h2o_zindos_directCIS_singlet.in, >>>> >>>> you can find the following output, >>>> >>>> | i-th | atom type | Unpaired electron population[a.u.]| >>>> Unpaired electron population: 0 O 2.220446e-15 >>>> Unpaired electron population: 1 H 0.000000e+00 >>>> Unpaired electron population: 2 H -1.110223e-15 >>>> >>>> . This is the output of unpaired electron population. >>>> I will send this log as 'h2o_zindos_directCIS_singlet.log'. >>>> >>>> The above case is an example. >>>> In the job that calculates Mulliken charge, the calculation >>>> of the unpaired electron population is executed. >>>> >>>> -- >>>> okymmolds >>>> _______________________________________________ >>>> MolDS-dev mailing list >>>> MolDS-dev ＠ lists.sourceforge.jp >>>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>> _______________________________________________ >>> MolDS-dev mailing list >>> MolDS-dev ＠ lists.sourceforge.jp >>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>> >> >> -- >> ------------------------- >> Michihiro Okuyama >> okymmolds ＠ gmail.com >> ------------------------- >> >> _______________________________________________ >> MolDS-dev mailing list >> MolDS-dev ＠ lists.sourceforge.jp >> http://lists.sourceforge.jp/mailman/listinfo/molds-dev > _______________________________________________ > MolDS-dev mailing list > MolDS-dev ＠ lists.sourceforge.jp > http://lists.sourceforge.jp/mailman/listinfo/molds-dev -------------- next part -------------- HTMLの添付ファイルを保管しました... URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20121109/03f0f6d0/attachment.htm From mikiya.fujii ＠ gmail.com Fri Nov 9 10:00:53 2012 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Fri, 9 Nov 2012 10:00:53 +0900 Subject: [Molds-dev] Unpaired_electron_population_code In-Reply-To: <509C51AC.7060406@gmail.com> References: <20121108111721.6e527055.okymmolds@gmail.com> <509C4C55.3010706@gmail.com> <509C51AC.7060406@gmail.com> Message-ID: Dear Michihiro, The following discussion is based on r1106. The term "UEP" means the unpaired electron population. 0)Basically, your coding is fine! 1)Although I do not know details of the UEP analysis, I think that the unpaired electron analysis is suitable as option. I wanna listen to your opinion. If UEP is one of the default analyses, you should modify the test suite in /trunk/test. If UEP is one of the option analyses, you should modify the input parser. 2)Can the UEP analysis be applied to both SCF and CI? 3)Is the "Cndo2::atomicElectronPopulation" needed to be a class-variable? If this UEP is not re-used except in SCF results, the "atomicElectronPopulation" is sufficient as a local variable of the "Cndo2::DoSCF" or else. 4)Line 1599 in Cndo2.cpp is not needed because the "Cndo2::atomicElectronPopulation" is initialized at the line 1593. I think the line 1580 guided you to miss-coding. Sorry, the line 1580 is my mistake, i.e., the 1580 is also not needed. I will fix to delete the line 1580. My best, Mikiya *************************************** Mikiya Fujii, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: fujii ＠ tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** 2012/11/9 okuyama : > > Dear Mr. Fujii > > Thanks for your E-mail. > O.K. > I thought that I'd like to confirm whether I could send the mail or not. > That's becauseI start using a new e-mailer. > > I'min holiday since last Saturday. > I'm going to start my job from next Monday. > So, I can take enough time to developthe Molds until it. > > I'm going to take abreakfast now. > > Best regards. > > M.Okuyama > > (2012/11/09 9:25), Mikiya Fujii wrote: >> Dear Michihiro, >> >> I received the mail with the attached files. >> Sorry, I could not check your coding yesterday. >> >> But I am checking your code just now! >> Please wait a moment. >> >> Anyway, are you in holiday? >> >> Best, >> Mikiya >> >> >> >> *************************************** >> Mikiya Fujii, Ph.D. >> >> Yamashita & Ushiyama Laboratory, >> Department of Chemical System Engineering, >> Faculty of Engineering, >> The University of Tokyo. >> >> tel&fax: +81-3-5841-7286 >> email: fujii ＠ tcl.t.u-tokyo.ac.jp >> HP: http://www.tcl.t.u-tokyo.ac.jp/ >> *************************************** >> >> >> 2012/11/9 Okuyama : >>> Dear Mr. Fujii >>> >>> After receiving the mail of the following contents, >>> I send the mail with attached files again to Molds-dev mailing list. >>> Could you receive my mail ? >>> >>> Best regards. >>> >>> M. Okuyama >>> >>> (2012年11月08日 12:35), Mikiya Fujii wrote: >>>> Dear M.Okuyama, >>>> >>>> Thanks for your contributions!!! >>>> However, the attached files were discarded by the mailing-list-system. >>>> >>>> I modified the setting of the mailing-list-system to allow attached files. >>>> Thus, please send the mail with the attached files again. >>>> >>>> My best, >>>> Mikiya >>>> >>>> >>>> >>>> >>>> >>>> >>>> *************************************** >>>> Mikiya Fujii, Ph.D. >>>> >>>> Yamashita & Ushiyama Laboratory, >>>> Department of Chemical System Engineering, >>>> Faculty of Engineering, >>>> The University of Tokyo. >>>> >>>> tel&fax: +81-3-5841-7286 >>>> email: fujii ＠ tcl.t.u-tokyo.ac.jp >>>> HP: http://www.tcl.t.u-tokyo.ac.jp/ >>>> *************************************** >>>> >>>> >>>> 2012/11/8 okymmolds : >>>>> Dear Fujii >>>>> >>>>> A patch file to calculate unpaired electron population >>>>> on ground state has been developed, where it's impossible to calculate >>>>> the population of excited states. orz >>>>> I send this patch file to you. >>>>> I wold like to get some opinion from you. >>>>> >>>>> Best regards. >>>>> >>>>> M.Okuyama >>>>> >>>>> ------- >>>>> How to patch by this patch file: >>>>> >>>>> In revision 1106 source code, you can introduce >>>>> a calculation of unpaired electron population to >>>>> your MolDS by the following command, >>>>> >>>>> mv unapired_pop.patch (work directory)/trunk/src >>>>> cd trunk/src >>>>> patch -p0 < unpaired_pop.patch >>>>> >>>>> --------- >>>>> About output of unpaired electron population: >>>>> For example, in src directory, if you execute the following command, >>>>> >>>>> ./MolDS.out ../test/h2o_zindos_directCIS_singlet.in, >>>>> >>>>> you can find the following output, >>>>> >>>>> | i-th | atom type | Unpaired electron population[a.u.]| >>>>> Unpaired electron population: 0 O 2.220446e-15 >>>>> Unpaired electron population: 1 H 0.000000e+00 >>>>> Unpaired electron population: 2 H -1.110223e-15 >>>>> >>>>> . This is the output of unpaired electron population. >>>>> I will send this log as 'h2o_zindos_directCIS_singlet.log'. >>>>> >>>>> The above case is an example. >>>>> In the job that calculates Mulliken charge, the calculation >>>>> of the unpaired electron population is executed. >>>>> >>>>> -- >>>>> okymmolds >>>>> _______________________________________________ >>>>> MolDS-dev mailing list >>>>> MolDS-dev ＠ lists.sourceforge.jp >>>>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>>> _______________________________________________ >>>> MolDS-dev mailing list >>>> MolDS-dev ＠ lists.sourceforge.jp >>>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>>> >>> >>> -- >>> ------------------------- >>> Michihiro Okuyama >>> okymmolds ＠ gmail.com >>> ------------------------- >>> >>> _______________________________________________ >>> MolDS-dev mailing list >>> MolDS-dev ＠ lists.sourceforge.jp >>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >> _______________________________________________ >> MolDS-dev mailing list >> MolDS-dev ＠ lists.sourceforge.jp >> http://lists.sourceforge.jp/mailman/listinfo/molds-dev > > -------------- next part -------------- > HTMLの添付ファイルを保管しました... > URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20121109/03f0f6d0/attachment.htm > _______________________________________________ > MolDS-dev mailing list > MolDS-dev ＠ lists.sourceforge.jp > http://lists.sourceforge.jp/mailman/listinfo/molds-dev From mikiya.fujii ＠ gmail.com Fri Nov 9 10:03:53 2012 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Fri, 9 Nov 2012 10:03:53 +0900 Subject: [Molds-dev] Unpaired_electron_population_code In-Reply-To: References: <20121108111721.6e527055.okymmolds@gmail.com> <509C4C55.3010706@gmail.com> <509C51AC.7060406@gmail.com> Message-ID: Dear Michihiro > 4)Line 1599 in Cndo2.cpp is not needed > because the "Cndo2::atomicElectronPopulation" is initialized at the line 1593. > I think the line 1580 guided you to miss-coding. > Sorry, the line 1580 is my mistake, i.e., the 1580 is also not needed. > I will fix to delete the line 1580. These line numbers are ones after your patch was applied to r1106. Mikiya *************************************** Mikiya Fujii, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: fujii ＠ tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** 2012/11/9 Mikiya Fujii : > Dear Michihiro, > > The following discussion is based on r1106. > The term "UEP" means the unpaired electron population. > > 0)Basically, your coding is fine! > > 1)Although I do not know details of the UEP analysis, > I think that the unpaired electron analysis is suitable as option. > I wanna listen to your opinion. > > If UEP is one of the default analyses, you should modify the test > suite in /trunk/test. > If UEP is one of the option analyses, you should modify the input parser. > > 2)Can the UEP analysis be applied to both SCF and CI? > > 3)Is the "Cndo2::atomicElectronPopulation" needed to be a class-variable? > If this UEP is not re-used except in SCF results, > the "atomicElectronPopulation" is sufficient as a local variable of > the "Cndo2::DoSCF" or else. > > 4)Line 1599 in Cndo2.cpp is not needed > because the "Cndo2::atomicElectronPopulation" is initialized at the line 1593. > I think the line 1580 guided you to miss-coding. > Sorry, the line 1580 is my mistake, i.e., the 1580 is also not needed. > I will fix to delete the line 1580. > > My best, > Mikiya > *************************************** > Mikiya Fujii, Ph.D. > > Yamashita & Ushiyama Laboratory, > Department of Chemical System Engineering, > Faculty of Engineering, > The University of Tokyo. > > tel&fax: +81-3-5841-7286 > email: fujii ＠ tcl.t.u-tokyo.ac.jp > HP: http://www.tcl.t.u-tokyo.ac.jp/ > *************************************** > > > 2012/11/9 okuyama : >> >> Dear Mr. Fujii >> >> Thanks for your E-mail. >> O.K. >> I thought that I'd like to confirm whether I could send the mail or not. >> That's becauseI start using a new e-mailer. >> >> I'min holiday since last Saturday. >> I'm going to start my job from next Monday. >> So, I can take enough time to developthe Molds until it. >> >> I'm going to take abreakfast now. >> >> Best regards. >> >> M.Okuyama >> >> (2012/11/09 9:25), Mikiya Fujii wrote: >>> Dear Michihiro, >>> >>> I received the mail with the attached files. >>> Sorry, I could not check your coding yesterday. >>> >>> But I am checking your code just now! >>> Please wait a moment. >>> >>> Anyway, are you in holiday? >>> >>> Best, >>> Mikiya >>> >>> >>> >>> *************************************** >>> Mikiya Fujii, Ph.D. >>> >>> Yamashita & Ushiyama Laboratory, >>> Department of Chemical System Engineering, >>> Faculty of Engineering, >>> The University of Tokyo. >>> >>> tel&fax: +81-3-5841-7286 >>> email: fujii ＠ tcl.t.u-tokyo.ac.jp >>> HP: http://www.tcl.t.u-tokyo.ac.jp/ >>> *************************************** >>> >>> >>> 2012/11/9 Okuyama : >>>> Dear Mr. Fujii >>>> >>>> After receiving the mail of the following contents, >>>> I send the mail with attached files again to Molds-dev mailing list. >>>> Could you receive my mail ? >>>> >>>> Best regards. >>>> >>>> M. Okuyama >>>> >>>> (2012年11月08日 12:35), Mikiya Fujii wrote: >>>>> Dear M.Okuyama, >>>>> >>>>> Thanks for your contributions!!! >>>>> However, the attached files were discarded by the mailing-list-system. >>>>> >>>>> I modified the setting of the mailing-list-system to allow attached files. >>>>> Thus, please send the mail with the attached files again. >>>>> >>>>> My best, >>>>> Mikiya >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> *************************************** >>>>> Mikiya Fujii, Ph.D. >>>>> >>>>> Yamashita & Ushiyama Laboratory, >>>>> Department of Chemical System Engineering, >>>>> Faculty of Engineering, >>>>> The University of Tokyo. >>>>> >>>>> tel&fax: +81-3-5841-7286 >>>>> email: fujii ＠ tcl.t.u-tokyo.ac.jp >>>>> HP: http://www.tcl.t.u-tokyo.ac.jp/ >>>>> *************************************** >>>>> >>>>> >>>>> 2012/11/8 okymmolds : >>>>>> Dear Fujii >>>>>> >>>>>> A patch file to calculate unpaired electron population >>>>>> on ground state has been developed, where it's impossible to calculate >>>>>> the population of excited states. orz >>>>>> I send this patch file to you. >>>>>> I wold like to get some opinion from you. >>>>>> >>>>>> Best regards. >>>>>> >>>>>> M.Okuyama >>>>>> >>>>>> ------- >>>>>> How to patch by this patch file: >>>>>> >>>>>> In revision 1106 source code, you can introduce >>>>>> a calculation of unpaired electron population to >>>>>> your MolDS by the following command, >>>>>> >>>>>> mv unapired_pop.patch (work directory)/trunk/src >>>>>> cd trunk/src >>>>>> patch -p0 < unpaired_pop.patch >>>>>> >>>>>> --------- >>>>>> About output of unpaired electron population: >>>>>> For example, in src directory, if you execute the following command, >>>>>> >>>>>> ./MolDS.out ../test/h2o_zindos_directCIS_singlet.in, >>>>>> >>>>>> you can find the following output, >>>>>> >>>>>> | i-th | atom type | Unpaired electron population[a.u.]| >>>>>> Unpaired electron population: 0 O 2.220446e-15 >>>>>> Unpaired electron population: 1 H 0.000000e+00 >>>>>> Unpaired electron population: 2 H -1.110223e-15 >>>>>> >>>>>> . This is the output of unpaired electron population. >>>>>> I will send this log as 'h2o_zindos_directCIS_singlet.log'. >>>>>> >>>>>> The above case is an example. >>>>>> In the job that calculates Mulliken charge, the calculation >>>>>> of the unpaired electron population is executed. >>>>>> >>>>>> -- >>>>>> okymmolds >>>>>> _______________________________________________ >>>>>> MolDS-dev mailing list >>>>>> MolDS-dev ＠ lists.sourceforge.jp >>>>>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>>>> _______________________________________________ >>>>> MolDS-dev mailing list >>>>> MolDS-dev ＠ lists.sourceforge.jp >>>>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>>>> >>>> >>>> -- >>>> ------------------------- >>>> Michihiro Okuyama >>>> okymmolds ＠ gmail.com >>>> ------------------------- >>>> >>>> _______________________________________________ >>>> MolDS-dev mailing list >>>> MolDS-dev ＠ lists.sourceforge.jp >>>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>> _______________________________________________ >>> MolDS-dev mailing list >>> MolDS-dev ＠ lists.sourceforge.jp >>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >> >> -------------- next part -------------- >> HTMLの添付ファイルを保管しました... >> URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20121109/03f0f6d0/attachment.htm >> _______________________________________________ >> MolDS-dev mailing list >> MolDS-dev ＠ lists.sourceforge.jp >> http://lists.sourceforge.jp/mailman/listinfo/molds-dev From okymmolds ＠ gmail.com Fri Nov 9 20:40:16 2012 From: okymmolds ＠ gmail.com (okuyama) Date: Fri, 09 Nov 2012 20:40:16 +0900 Subject: [Molds-dev] Unpaired_electron_population_code In-Reply-To: References: <20121108111721.6e527055.okymmolds@gmail.com> <509C4C55.3010706@gmail.com> <509C51AC.7060406@gmail.com> Message-ID: <509CEBA0.6050804@gmail.com> Dear Mr. Fujii Thanks for your response and opinions. I will write my response under your question as follows. (2012/11/09 10:00), Mikiya Fujii wrote: > Dear Michihiro, > > The following discussion is based on r1106. > The term "UEP" means the unpaired electron population. > > 0)Basically, your coding is fine! Thanks ! I'm glad. > > 1)Although I do not know details of the UEP analysis, > I think that the unpaired electron analysis is suitable as option. > I wanna listen to your opinion. I think so too. I think that I'd like to be able to calculate the UEP analysis if user hope the analysis. In that case, we need to consider about the detail of new options. In this point, I'd like to hear your opinions, where I will also consider about that. > > If UEP is one of the default analyses, you should modify the test > suite in /trunk/test. > If UEP is one of the option analyses, you should modify the input parser. > > 2)Can the UEP analysis be applied to both SCF and CI? Yes, it can theoretically. However, in the implementation at my patch file, the UEP analysis can't be applied to CI. > > 3)Is the "Cndo2::atomicElectronPopulation" needed to be a class-variable? > If this UEP is not re-used except in SCF results, > the "atomicElectronPopulation" is sufficient as a local variable of > the "Cndo2::DoSCF" or else. My answer for this question is nothing. That's because there are two consideration as follows: 1) The UEP analysis should be used at a system involved electron correlation. The reason why the UEP becomes zero in the SCF as the Hartree-Fock method not included electron correlation. I guess the SCF method in the MolDS does not include electron correlation. So, the UEP analysis needs to be used at methods without the SCF. In the MolDS, is the calculation including electron correlation only the CI ? 2) I can't understand deeply a concept of class at the C++ yet. In this point, I probably need to have a chance to do a more discussion by using the E-mail etc. > > 4)Line 1599 in Cndo2.cpp is not needed > because the "Cndo2::atomicElectronPopulation" is initialized at the line 1593. > I think the line 1580 guided you to miss-coding. > Sorry, the line 1580 is my mistake, i.e., the 1580 is also not needed. > I will fix to delete the line 1580. O.K. Best regards. M. Okuyama. > > My best, > Mikiya > *************************************** > Mikiya Fujii, Ph.D. > > Yamashita & Ushiyama Laboratory, > Department of Chemical System Engineering, > Faculty of Engineering, > The University of Tokyo. > > tel&fax: +81-3-5841-7286 > email: fujii ＠ tcl.t.u-tokyo.ac.jp > HP: http://www.tcl.t.u-tokyo.ac.jp/ > *************************************** > > > 2012/11/9 okuyama : >> Dear Mr. Fujii >> >> Thanks for your E-mail. >> O.K. >> I thought that I'd like to confirm whether I could send the mail or not. >> That's becauseI start using a new e-mailer. >> >> I'min holiday since last Saturday. >> I'm going to start my job from next Monday. >> So, I can take enough time to developthe Molds until it. >> >> I'm going to take abreakfast now. >> >> Best regards. >> >> M.Okuyama >> >> (2012/11/09 9:25), Mikiya Fujii wrote: >>> Dear Michihiro, >>> >>> I received the mail with the attached files. >>> Sorry, I could not check your coding yesterday. >>> >>> But I am checking your code just now! >>> Please wait a moment. >>> >>> Anyway, are you in holiday? >>> >>> Best, >>> Mikiya >>> >>> >>> >>> *************************************** >>> Mikiya Fujii, Ph.D. >>> >>> Yamashita & Ushiyama Laboratory, >>> Department of Chemical System Engineering, >>> Faculty of Engineering, >>> The University of Tokyo. >>> >>> tel&fax: +81-3-5841-7286 >>> email: fujii ＠ tcl.t.u-tokyo.ac.jp >>> HP: http://www.tcl.t.u-tokyo.ac.jp/ >>> *************************************** >>> >>> >>> 2012/11/9 Okuyama : >>>> Dear Mr. Fujii >>>> >>>> After receiving the mail of the following contents, >>>> I send the mail with attached files again to Molds-dev mailing list. >>>> Could you receive my mail ? >>>> >>>> Best regards. >>>> >>>> M. Okuyama >>>> >>>> (2012年11月08日 12:35), Mikiya Fujii wrote: >>>>> Dear M.Okuyama, >>>>> >>>>> Thanks for your contributions!!! >>>>> However, the attached files were discarded by the mailing-list-system. >>>>> >>>>> I modified the setting of the mailing-list-system to allow attached files. >>>>> Thus, please send the mail with the attached files again. >>>>> >>>>> My best, >>>>> Mikiya >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> *************************************** >>>>> Mikiya Fujii, Ph.D. >>>>> >>>>> Yamashita & Ushiyama Laboratory, >>>>> Department of Chemical System Engineering, >>>>> Faculty of Engineering, >>>>> The University of Tokyo. >>>>> >>>>> tel&fax: +81-3-5841-7286 >>>>> email: fujii ＠ tcl.t.u-tokyo.ac.jp >>>>> HP: http://www.tcl.t.u-tokyo.ac.jp/ >>>>> *************************************** >>>>> >>>>> >>>>> 2012/11/8 okymmolds : >>>>>> Dear Fujii >>>>>> >>>>>> A patch file to calculate unpaired electron population >>>>>> on ground state has been developed, where it's impossible to calculate >>>>>> the population of excited states. orz >>>>>> I send this patch file to you. >>>>>> I wold like to get some opinion from you. >>>>>> >>>>>> Best regards. >>>>>> >>>>>> M.Okuyama >>>>>> >>>>>> ------- >>>>>> How to patch by this patch file: >>>>>> >>>>>> In revision 1106 source code, you can introduce >>>>>> a calculation of unpaired electron population to >>>>>> your MolDS by the following command, >>>>>> >>>>>> mv unapired_pop.patch (work directory)/trunk/src >>>>>> cd trunk/src >>>>>> patch -p0 < unpaired_pop.patch >>>>>> >>>>>> --------- >>>>>> About output of unpaired electron population: >>>>>> For example, in src directory, if you execute the following command, >>>>>> >>>>>> ./MolDS.out ../test/h2o_zindos_directCIS_singlet.in, >>>>>> >>>>>> you can find the following output, >>>>>> >>>>>> | i-th | atom type | Unpaired electron population[a.u.]| >>>>>> Unpaired electron population: 0 O 2.220446e-15 >>>>>> Unpaired electron population: 1 H 0.000000e+00 >>>>>> Unpaired electron population: 2 H -1.110223e-15 >>>>>> >>>>>> . This is the output of unpaired electron population. >>>>>> I will send this log as 'h2o_zindos_directCIS_singlet.log'. >>>>>> >>>>>> The above case is an example. >>>>>> In the job that calculates Mulliken charge, the calculation >>>>>> of the unpaired electron population is executed. >>>>>> >>>>>> -- >>>>>> okymmolds >>>>>> _______________________________________________ >>>>>> MolDS-dev mailing list >>>>>> MolDS-dev ＠ lists.sourceforge.jp >>>>>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>>>> _______________________________________________ >>>>> MolDS-dev mailing list >>>>> MolDS-dev ＠ lists.sourceforge.jp >>>>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>>>> >>>> -- >>>> ------------------------- >>>> Michihiro Okuyama >>>> okymmolds ＠ gmail.com >>>> ------------------------- >>>> >>>> _______________________________________________ >>>> MolDS-dev mailing list >>>> MolDS-dev ＠ lists.sourceforge.jp >>>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>> _______________________________________________ >>> MolDS-dev mailing list >>> MolDS-dev ＠ lists.sourceforge.jp >>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >> -------------- next part -------------- >> HTMLの添付ファイルを保管しました... >> URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20121109/03f0f6d0/attachment.htm >> _______________________________________________ >> MolDS-dev mailing list >> MolDS-dev ＠ lists.sourceforge.jp >> http://lists.sourceforge.jp/mailman/listinfo/molds-dev > _______________________________________________ > MolDS-dev mailing list > MolDS-dev ＠ lists.sourceforge.jp > http://lists.sourceforge.jp/mailman/listinfo/molds-dev From mikiya.fujii ＠ gmail.com Mon Nov 12 11:36:27 2012 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Mon, 12 Nov 2012 11:36:27 +0900 Subject: [Molds-dev] Unpaired_electron_population_code In-Reply-To: <509CEBA0.6050804@gmail.com> References: <20121108111721.6e527055.okymmolds@gmail.com> <509C4C55.3010706@gmail.com> <509C51AC.7060406@gmail.com> <509CEBA0.6050804@gmail.com> Message-ID: Dear M. Okuyama, Sorry to late. Last weekend, I had been to Izu by the laboratory travel. > In the MolDS, is the calculation including electron correlation only the > CI ? YES. In this stage, we have a plan to implement SCF and CIS only. > I guess the SCF method in the MolDS does not include electron correlation. > So, the UEP analysis needs to be used at methods without the SCF. YES. SCF in MolDS does not include any electron correlation. Therefore, it seems better that UEP is implemented in CIS-module (i.e. ZndoS::CalcCISProperties() and ZndoS::OutputCISResults()) than SCF. To implement UEP as one of the additional option analyses, "exciton_energies" which is one of the CIS-options may be of best reference. Beside, I think there are no problem to made "atomicElectronPopulation" be a class-variable of Cndo2 like as "Cndo2::freeExcitonEnergiesCIS". But, take care the timing of Malloc and Free of "atomicElectronPopulation". The same treatments with Malloc and Free of "Cndo2::freeExcitonEnergiesCIS" in "ZindoS" are good for UEP also. My best, Mikia *************************************** Mikiya Fujii, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: fujii ＠ tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** 2012/11/9 okuyama : > > Dear Mr. Fujii > > Thanks for your response and opinions. > I will write my response under your question as follows. > > (2012/11/09 10:00), Mikiya Fujii wrote: >> Dear Michihiro, >> >> The following discussion is based on r1106. >> The term "UEP" means the unpaired electron population. >> >> 0)Basically, your coding is fine! > Thanks ! I'm glad. >> >> 1)Although I do not know details of the UEP analysis, >> I think that the unpaired electron analysis is suitable as option. >> I wanna listen to your opinion. > I think so too. > I think that I'd like to be able to calculate the UEP analysis if user > hope the analysis. > In that case, we need to consider about the detail of new options. > In this point, I'd like to hear your opinions, > where I will also consider about that. >> >> If UEP is one of the default analyses, you should modify the test >> suite in /trunk/test. >> If UEP is one of the option analyses, you should modify the input parser. >> >> 2)Can the UEP analysis be applied to both SCF and CI? > Yes, it can theoretically. However, in the implementation at my patch file, > the UEP analysis can't be applied to CI. > >> >> 3)Is the "Cndo2::atomicElectronPopulation" needed to be a class-variable? >> If this UEP is not re-used except in SCF results, >> the "atomicElectronPopulation" is sufficient as a local variable of >> the "Cndo2::DoSCF" or else. > My answer for this question is nothing. > That's because there are two consideration as follows: > 1) The UEP analysis should be used at a system involved electron > correlation. > The reason why the UEP becomes zero in the SCF > as the Hartree-Fock method not included electron correlation. > I guess the SCF method in the MolDS does not include electron correlation. > So, the UEP analysis needs to be used at methods without the SCF. > In the MolDS, is the calculation including electron correlation only the > CI ? > 2) I can't understand deeply a concept of class at the C++ yet. > > In this point, I probably need to have a chance to do a more discussion > by using the E-mail etc. >> >> 4)Line 1599 in Cndo2.cpp is not needed >> because the "Cndo2::atomicElectronPopulation" is initialized at the line 1593. >> I think the line 1580 guided you to miss-coding. >> Sorry, the line 1580 is my mistake, i.e., the 1580 is also not needed. >> I will fix to delete the line 1580. > O.K. > > Best regards. > > M. Okuyama. >> >> My best, >> Mikiya >> *************************************** >> Mikiya Fujii, Ph.D. >> >> Yamashita & Ushiyama Laboratory, >> Department of Chemical System Engineering, >> Faculty of Engineering, >> The University of Tokyo. >> >> tel&fax: +81-3-5841-7286 >> email: fujii ＠ tcl.t.u-tokyo.ac.jp >> HP: http://www.tcl.t.u-tokyo.ac.jp/ >> *************************************** >> >> >> 2012/11/9 okuyama : >>> Dear Mr. Fujii >>> >>> Thanks for your E-mail. >>> O.K. >>> I thought that I'd like to confirm whether I could send the mail or not. >>> That's becauseI start using a new e-mailer. >>> >>> I'min holiday since last Saturday. >>> I'm going to start my job from next Monday. >>> So, I can take enough time to developthe Molds until it. >>> >>> I'm going to take abreakfast now. >>> >>> Best regards. >>> >>> M.Okuyama >>> >>> (2012/11/09 9:25), Mikiya Fujii wrote: >>>> Dear Michihiro, >>>> >>>> I received the mail with the attached files. >>>> Sorry, I could not check your coding yesterday. >>>> >>>> But I am checking your code just now! >>>> Please wait a moment. >>>> >>>> Anyway, are you in holiday? >>>> >>>> Best, >>>> Mikiya >>>> >>>> >>>> >>>> *************************************** >>>> Mikiya Fujii, Ph.D. >>>> >>>> Yamashita & Ushiyama Laboratory, >>>> Department of Chemical System Engineering, >>>> Faculty of Engineering, >>>> The University of Tokyo. >>>> >>>> tel&fax: +81-3-5841-7286 >>>> email: fujii ＠ tcl.t.u-tokyo.ac.jp >>>> HP: http://www.tcl.t.u-tokyo.ac.jp/ >>>> *************************************** >>>> >>>> >>>> 2012/11/9 Okuyama : >>>>> Dear Mr. Fujii >>>>> >>>>> After receiving the mail of the following contents, >>>>> I send the mail with attached files again to Molds-dev mailing list. >>>>> Could you receive my mail ? >>>>> >>>>> Best regards. >>>>> >>>>> M. Okuyama >>>>> >>>>> (2012年11月08日 12:35), Mikiya Fujii wrote: >>>>>> Dear M.Okuyama, >>>>>> >>>>>> Thanks for your contributions!!! >>>>>> However, the attached files were discarded by the mailing-list-system. >>>>>> >>>>>> I modified the setting of the mailing-list-system to allow attached files. >>>>>> Thus, please send the mail with the attached files again. >>>>>> >>>>>> My best, >>>>>> Mikiya >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> *************************************** >>>>>> Mikiya Fujii, Ph.D. >>>>>> >>>>>> Yamashita & Ushiyama Laboratory, >>>>>> Department of Chemical System Engineering, >>>>>> Faculty of Engineering, >>>>>> The University of Tokyo. >>>>>> >>>>>> tel&fax: +81-3-5841-7286 >>>>>> email: fujii ＠ tcl.t.u-tokyo.ac.jp >>>>>> HP: http://www.tcl.t.u-tokyo.ac.jp/ >>>>>> *************************************** >>>>>> >>>>>> >>>>>> 2012/11/8 okymmolds : >>>>>>> Dear Fujii >>>>>>> >>>>>>> A patch file to calculate unpaired electron population >>>>>>> on ground state has been developed, where it's impossible to calculate >>>>>>> the population of excited states. orz >>>>>>> I send this patch file to you. >>>>>>> I wold like to get some opinion from you. >>>>>>> >>>>>>> Best regards. >>>>>>> >>>>>>> M.Okuyama >>>>>>> >>>>>>> ------- >>>>>>> How to patch by this patch file: >>>>>>> >>>>>>> In revision 1106 source code, you can introduce >>>>>>> a calculation of unpaired electron population to >>>>>>> your MolDS by the following command, >>>>>>> >>>>>>> mv unapired_pop.patch (work directory)/trunk/src >>>>>>> cd trunk/src >>>>>>> patch -p0 < unpaired_pop.patch >>>>>>> >>>>>>> --------- >>>>>>> About output of unpaired electron population: >>>>>>> For example, in src directory, if you execute the following command, >>>>>>> >>>>>>> ./MolDS.out ../test/h2o_zindos_directCIS_singlet.in, >>>>>>> >>>>>>> you can find the following output, >>>>>>> >>>>>>> | i-th | atom type | Unpaired electron population[a.u.]| >>>>>>> Unpaired electron population: 0 O 2.220446e-15 >>>>>>> Unpaired electron population: 1 H 0.000000e+00 >>>>>>> Unpaired electron population: 2 H -1.110223e-15 >>>>>>> >>>>>>> . This is the output of unpaired electron population. >>>>>>> I will send this log as 'h2o_zindos_directCIS_singlet.log'. >>>>>>> >>>>>>> The above case is an example. >>>>>>> In the job that calculates Mulliken charge, the calculation >>>>>>> of the unpaired electron population is executed. >>>>>>> >>>>>>> -- >>>>>>> okymmolds >>>>>>> _______________________________________________ >>>>>>> MolDS-dev mailing list >>>>>>> MolDS-dev ＠ lists.sourceforge.jp >>>>>>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>>>>> _______________________________________________ >>>>>> MolDS-dev mailing list >>>>>> MolDS-dev ＠ lists.sourceforge.jp >>>>>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>>>>> >>>>> -- >>>>> ------------------------- >>>>> Michihiro Okuyama >>>>> okymmolds ＠ gmail.com >>>>> ------------------------- >>>>> >>>>> _______________________________________________ >>>>> MolDS-dev mailing list >>>>> MolDS-dev ＠ lists.sourceforge.jp >>>>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>>> _______________________________________________ >>>> MolDS-dev mailing list >>>> MolDS-dev ＠ lists.sourceforge.jp >>>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >>> -------------- next part -------------- >>> HTMLの添付ファイルを保管しました... >>> URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20121109/03f0f6d0/attachment.htm >>> _______________________________________________ >>> MolDS-dev mailing list >>> MolDS-dev ＠ lists.sourceforge.jp >>> http://lists.sourceforge.jp/mailman/listinfo/molds-dev >> _______________________________________________ >> MolDS-dev mailing list >> MolDS-dev ＠ lists.sourceforge.jp >> http://lists.sourceforge.jp/mailman/listinfo/molds-dev > > _______________________________________________ > MolDS-dev mailing list > MolDS-dev ＠ lists.sourceforge.jp > http://lists.sourceforge.jp/mailman/listinfo/molds-dev From noreply ＠ sourceforge.jp Tue Nov 13 12:26:42 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 13 Nov 2012 12:26:42 +0900 Subject: [Molds-dev] [molds] #30083: Avoid overflow of "int" in the "MallocerFrrer" Message-ID: <1352777202.911301.13626.nullmailer@sourceforge.jp> #30083: Avoid overflow of "int" in the "MallocerFrrer" Open Date: 2012-11-13 12:26 Last Update: 2012-11-13 12:26 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30083 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30083 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-13 12:26 Update by: mikiya_fujii * New Ticket "Avoid overflow of "int" in the "MallocerFrrer"" created --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: オープン Priority: 6 MileStone: ver0.2 Component: (未割り当て) Severity: 6 Resolution: なし --------------------------------------------------------------------- Ticket details: 1)Type of arguments for size of array is modified to size_t from int 2)To avoid overflow, way to calculate "requiredMalloc" is modified to double requiredMalloc = static_cast(size1); *static_cast(size2); *static_cast(sizeof(T)); 3)To check the amount of allocated heap in more detail, variables for address should be counted in the "requiredMalloc" -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30083 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30083 From noreply ＠ sourceforge.jp Tue Nov 13 12:27:30 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 13 Nov 2012 12:27:30 +0900 Subject: [Molds-dev] [molds] #30083: Avoid overflow of "int" in the "MallocerFrrer" Message-ID: <1352777250.756602.26152.nullmailer@sourceforge.jp> #30083: Avoid overflow of "int" in the "MallocerFrrer" Open Date: 2012-11-13 12:26 Last Update: 2012-11-13 12:27 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30083 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30083 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-13 12:27 Update by: mikiya_fujii * Details Updated --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: オープン Priority: 6 MileStone: ver0.2 Component: (未割り当て) Severity: 6 Resolution: なし --------------------------------------------------------------------- Ticket details: 1)Type of arguments for size of array is modified to size_t from int[[BR]] 2)To avoid overflow, way to calculate "requiredMalloc" is modified to [[BR]] {{{ double requiredMalloc = static_cast(size1); *static_cast(size2); *static_cast(sizeof(T)); }}} 3)To check the amount of allocated heap in more detail, variables for address should be counted in the "requiredMalloc" -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30083 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30083 From noreply ＠ sourceforge.jp Wed Nov 14 17:52:38 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 14 Nov 2012 17:52:38 +0900 Subject: [Molds-dev] [molds] #30083: Avoid overflow of "int" in the "MallocerFrrer" Message-ID: <1352883158.573980.25450.nullmailer@sourceforge.jp> #30083: Avoid overflow of "int" in the "MallocerFrrer" Open Date: 2012-11-13 12:26 Last Update: 2012-11-14 17:52 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30083 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30083 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-14 17:52 Update by: mikiya_fujii * Ticket Close date set to 2012-11-14 17:52 * 状況 Update from オープン to 完了. * 解決法 Update from なし to 修正済み. Comment: Fixed at r1117. Then MallocerFreer is refactored at r1118. --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: 完了 Priority: 6 MileStone: ver0.2 Component: (未割り当て) Severity: 6 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: 1)Type of arguments for size of array is modified to size_t from int[[BR]] 2)To avoid overflow, way to calculate "requiredMalloc" is modified to [[BR]] {{{ double requiredMalloc = static_cast(size1); *static_cast(size2); *static_cast(sizeof(T)); }}} 3)To check the amount of allocated heap in more detail, variables for address should be counted in the "requiredMalloc" -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30083 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30083 From noreply ＠ sourceforge.jp Thu Nov 15 18:28:02 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 15 Nov 2012 18:28:02 +0900 Subject: [Molds-dev] [molds] #30111: Parallelize ZindoS::GetElectronicTransitionDipoleMoment Message-ID: <1352971682.057052.20430.nullmailer@sourceforge.jp> #30111: Parallelize ZindoS::GetElectronicTransitionDipoleMoment Open Date: 2012-11-15 18:28 Last Update: 2012-11-15 18:28 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30111 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30111 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-15 18:28 Update by: mikiya_fujii * New Ticket "Parallelize ZindoS::GetElectronicTransitionDipoleMoment" created --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: オープン Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Parallelize ZindoS::GetElectronicTransitionDipoleMoment -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30111 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30111 From mikiya.fujii ＠ gmail.com Thu Nov 15 18:30:27 2012 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Thu, 15 Nov 2012 18:30:27 +0900 Subject: [Molds-dev] The CIS module take a long long time because this module is not parallelized well! Message-ID: Dear all, CIS of MolDS is not parallelized, especially, the method to calculate transition dipole moments is not parallelized! So, the CIS module take a long long time. Sorry this is a my misstake. I will paralellize the CIS module as soon as possible. Ticket #30111: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30111#preview My best, Mikiya *************************************** Mikiya Fujii, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: fujii ＠ tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** From noreply ＠ sourceforge.jp Fri Nov 16 17:53:08 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Fri, 16 Nov 2012 17:53:08 +0900 Subject: [Molds-dev] [molds] #30111: Parallelize ZindoS::GetElectronicTransitionDipoleMoment Message-ID: <1353055988.431946.13682.nullmailer@sourceforge.jp> #30111: Parallelize ZindoS::GetElectronicTransitionDipoleMoment Open Date: 2012-11-15 18:28 Last Update: 2012-11-16 17:53 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30111 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30111 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-16 17:53 Update by: mikiya_fujii * Details Updated --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: オープン Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Parallelize ZindoS::GetElectronicTransitionDipoleMoment[[BR]] Parallelization of the module to calculate dipole moment of the ground state should be changed to be more efficient for many core machines. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30111 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30111 From noreply ＠ sourceforge.jp Fri Nov 16 17:53:22 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Fri, 16 Nov 2012 17:53:22 +0900 Subject: [Molds-dev] [molds] #30111: Parallelize ZindoS::GetElectronicTransitionDipoleMoment Message-ID: <1353056002.974587.18624.nullmailer@sourceforge.jp> #30111: Parallelize ZindoS::GetElectronicTransitionDipoleMoment Open Date: 2012-11-15 18:28 Last Update: 2012-11-16 17:53 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30111 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30111 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-16 17:53 Update by: mikiya_fujii * Details Updated --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: オープン Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Parallelize ZindoS::GetElectronicTransitionDipoleMoment.[[BR]] Parallelization of the module to calculate dipole moment of the ground state should be also changed to be more efficient for many core machines. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30111 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30111 From noreply ＠ sourceforge.jp Fri Nov 16 19:09:51 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Fri, 16 Nov 2012 19:09:51 +0900 Subject: [Molds-dev] [molds] #30111: Parallelize ZindoS::GetElectronicTransitionDipoleMoment Message-ID: <1353060591.949266.5564.nullmailer@sourceforge.jp> #30111: Parallelize ZindoS::GetElectronicTransitionDipoleMoment Open Date: 2012-11-15 18:28 Last Update: 2012-11-16 19:09 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30111 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30111 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-16 19:09 Update by: mikiya_fujii * Ticket Close date set to 2012-11-16 19:09 * 状況 Update from オープン to 完了. Comment: Fixed at r1120. This palatalization is openMP. --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: 完了 Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Parallelize ZindoS::GetElectronicTransitionDipoleMoment.[[BR]] Parallelization of the module to calculate dipole moment of the ground state should be also changed to be more efficient for many core machines. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30111 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30111 From noreply ＠ sourceforge.jp Fri Nov 16 19:09:58 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Fri, 16 Nov 2012 19:09:58 +0900 Subject: [Molds-dev] [molds] #30111: Parallelize ZindoS::GetElectronicTransitionDipoleMoment Message-ID: <1353060598.770608.24365.nullmailer@sourceforge.jp> #30111: Parallelize ZindoS::GetElectronicTransitionDipoleMoment Open Date: 2012-11-15 18:28 Last Update: 2012-11-16 19:09 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30111 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30111 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-16 19:09 Update by: mikiya_fujii * 解決法 Update from なし to 修正済み. --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: 完了 Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Parallelize ZindoS::GetElectronicTransitionDipoleMoment.[[BR]] Parallelization of the module to calculate dipole moment of the ground state should be also changed to be more efficient for many core machines. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30111 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30111 From mikiya.fujii ＠ gmail.com Fri Nov 16 19:10:59 2012 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Fri, 16 Nov 2012 19:10:59 +0900 Subject: [Molds-dev] The CIS module take a long long time because this module is not parallelized well! In-Reply-To: References: Message-ID: Dear all, I fixed this #30111 at r11120. My best, Mikiya *************************************** Mikiya Fujii, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: fujii ＠ tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** 2012/11/15 Mikiya Fujii : > Dear all, > > CIS of MolDS is not parallelized, especially, the method to calculate > transition dipole moments is not parallelized! > So, the CIS module take a long long time. > Sorry this is a my misstake. > I will paralellize the CIS module as soon as possible. > Ticket #30111: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30111#preview > > My best, > Mikiya > > *************************************** > Mikiya Fujii, Ph.D. > > Yamashita & Ushiyama Laboratory, > Department of Chemical System Engineering, > Faculty of Engineering, > The University of Tokyo. > > tel&fax: +81-3-5841-7286 > email: fujii ＠ tcl.t.u-tokyo.ac.jp > HP: http://www.tcl.t.u-tokyo.ac.jp/ > *************************************** From noreply ＠ sourceforge.jp Tue Nov 20 01:04:02 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 20 Nov 2012 01:04:02 +0900 Subject: [Molds-dev] [molds] #30153: Boltzman-distributor Message-ID: <1353341042.657931.13476.nullmailer@sourceforge.jp> #30153: Boltzman-distributor Open Date: 2012-11-20 01:04 Last Update: 2012-11-20 01:04 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30153 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30153 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-20 01:04 Update by: mikiya_fujii * New Ticket "Boltzman-distributor" created --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: オープン Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Boltzman-distributor -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30153 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30153 From noreply ＠ sourceforge.jp Tue Nov 20 01:08:00 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 20 Nov 2012 01:08:00 +0900 Subject: [Molds-dev] [molds] #30154: dos Message-ID: <1353341280.479689.10192.nullmailer@sourceforge.jp> #30154: dos Open Date: 2012-11-20 01:07 Last Update: 2012-11-20 01:07 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30154 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30154 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-20 01:08 Update by: mikiya_fujii * New Ticket "dos" created --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: (未割り当て) Type: 機能リクエスト Status: オープン Priority: 5 - 中 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: approximated dos written in "Polymer Engineering and science, 47, 1359(2007)" http://onlinelibrary.wiley.com/doi/10.1002/pen.20820/abstract -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30154 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30154 From noreply ＠ sourceforge.jp Tue Nov 20 17:45:21 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 20 Nov 2012 17:45:21 +0900 Subject: [Molds-dev] [molds] #30161: overfolw of int in "Lapack.cpp" Message-ID: <1353401121.955214.28908.nullmailer@sourceforge.jp> #30161: overfolw of int in "Lapack.cpp" Open Date: 2012-11-20 17:45 Last Update: 2012-11-20 17:45 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30161 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30161 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-20 17:45 Update by: mikiya_fujii * New Ticket "overfolw of int in "Lapack.cpp"" created --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: バグ Status: オープン Priority: 6 MileStone: ver0.2 Component: (未割り当て) Severity: 6 Resolution: なし --------------------------------------------------------------------- Ticket details: overfolw of int in "Lapack.cpp"[[BR]] Type of arguments for size of array should be modified to size_t from int -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30161 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30161 From noreply ＠ sourceforge.jp Mon Nov 26 16:53:12 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Mon, 26 Nov 2012 16:53:12 +0900 Subject: [Molds-dev] [molds] #29877: Add dsyr routine into BLAS wrapper Message-ID: <1353916392.489214.552.nullmailer@sourceforge.jp> #29877: Add dsyr routine into BLAS wrapper Open Date: 2012-10-18 18:53 Last Update: 2012-11-26 16:53 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=29877 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=29877 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-26 16:53 Update by: ktns * Ticket Close date set to 2012-11-26 16:53 * 状況 Update from オープン to 完了. Comment: Implemented and fixed bugs on r1125 . --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: サポートリクエスト Status: 完了 Priority: 4 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Implement dsyr routine wrapper function into BLAS wrapper module. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=29877 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=29877 From noreply ＠ sourceforge.jp Mon Nov 26 16:54:22 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Mon, 26 Nov 2012 16:54:22 +0900 Subject: [Molds-dev] [molds] #29878: Add daxpy routine into BLAS wrapper Message-ID: <1353916462.270719.25496.nullmailer@sourceforge.jp> #29878: Add daxpy routine into BLAS wrapper Open Date: 2012-10-18 18:57 Last Update: 2012-11-26 16:54 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=29878 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=29878 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-26 16:54 Update by: ktns * Ticket Close date set to 2012-11-26 16:54 * 状況 Update from オープン to 完了. --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: サポートリクエスト Status: 完了 Priority: 4 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Implement a wrapper function for the daxpy routine into BLAS wrapper module. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=29878 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=29878 From noreply ＠ sourceforge.jp Mon Nov 26 16:56:58 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Mon, 26 Nov 2012 16:56:58 +0900 Subject: [Molds-dev] [molds] #29876: Add dsymv routine into BLAS wrapper Message-ID: <1353916618.456127.21769.nullmailer@sourceforge.jp> #29876: Add dsymv routine into BLAS wrapper Open Date: 2012-10-18 18:51 Last Update: 2012-11-26 16:56 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=29876 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=29876 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-26 16:56 Update by: ktns * Ticket Close date set to 2012-11-26 16:56 * 状況 Update from オープン to 完了. Comment: Fixed bug on r1129 . --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: サポートリクエスト Status: 完了 Priority: 4 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Implement dsymv wrapper function in BLAS wrapper module. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=29876 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=29876 From noreply ＠ sourceforge.jp Mon Nov 26 20:51:13 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Mon, 26 Nov 2012 20:51:13 +0900 Subject: [Molds-dev] [molds] #28764: BFGS optimizer Message-ID: <1353930673.758067.30279.nullmailer@sourceforge.jp> #28764: BFGS optimizer Open Date: 2012-06-16 22:01 Last Update: 2012-11-26 20:51 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=28764 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=28764 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-26 20:51 Update by: ktns * Ticket Close date set to 2012-11-26 20:51 * 状況 Update from オープン to 完了. Comment: Initial trust radius and maximum step size are now read from the input file. Implemented at r1131 --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: 機能リクエスト Status: 完了 Priority: 3 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Optimizer class using BFGS method -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=28764 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=28764 From noreply ＠ sourceforge.jp Mon Nov 26 21:23:45 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Mon, 26 Nov 2012 21:23:45 +0900 Subject: [Molds-dev] [molds] #30044: Overloaded constructor of MolDSException for boost::format Message-ID: <1353932625.033509.15996.nullmailer@sourceforge.jp> #30044: Overloaded constructor of MolDSException for boost::format Open Date: 2012-11-07 23:35 Last Update: 2012-11-26 21:23 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30044 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30044 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-26 21:23 Update by: ktns * Ticket Close date set to 2012-11-26 21:23 * 状況 Update from オープン to 完了. * 解決法 Update from なし to 修正済み. Comment: Implemented on r1108 --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: パッチ Status: 完了 Priority: 3 MileStone: (未割り当て) Component: (未割り当て) Severity: 3 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: {{{ code cpp throw MolDSException(boost::format("%s: %d\n") % str % num); }}} -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30044 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30044 From mikiya.fujii ＠ gmail.com Mon Nov 26 22:50:20 2012 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Mon, 26 Nov 2012 22:50:20 +0900 Subject: [Molds-dev] Documentation of the BFGS-optimizer Message-ID: Dear ktns, Congratulation for finishing the implementation of the BFGS at r1131!! But, before closing the ticket 28764, I wanna ask you to write how to set the parameters ("initialtrustradius" and "maxnormstep") in input files to the doc/README.txt. The default values of these parameters should be also written in doc/README.txt. Furthermore, keywords in input files should consist of some words which are combined with "_", i.e. "initial_trust_radius" and "max_norm_step". My best, Mikiya *************************************** Mikiya Fujii, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: fujii ＠ tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** ---------- Forwarded message ---------- From: SourceForge Ticket System Date: 2012/11/26 Subject: [Molds-dev] [molds] #28764: BFGS optimizer To: SourceForge Ticket System #28764: BFGS optimizer Open Date: 2012-06-16 22:01 Last Update: 2012-11-26 20:51 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=28764 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=28764 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-26 20:51 Update by: ktns * Ticket Close date set to 2012-11-26 20:51 * 状況 Update from オープン to 完了. Comment: Initial trust radius and maximum step size are now read from the input file. Implemented at r1131 --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: 機能リクエスト Status: 完了 Priority: 3 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Optimizer class using BFGS method -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=28764 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=28764 _______________________________________________ MolDS-dev mailing list MolDS-dev ＠ lists.sourceforge.jp http://lists.sourceforge.jp/mailman/listinfo/molds-dev From noreply ＠ sourceforge.jp Wed Nov 28 13:40:57 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 28 Nov 2012 13:40:57 +0900 Subject: [Molds-dev] [molds] #30207: Versions of OpneBLAS and Boost should not been assigned in Makefile Message-ID: <1354077657.619054.3045.nullmailer@sourceforge.jp> #30207: Versions of OpneBLAS and Boost should not been assigned in Makefile Open Date: 2012-11-28 13:40 Last Update: 2012-11-28 13:40 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30207 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30207 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-28 13:40 Update by: mikiya_fujii * New Ticket "Versions of OpneBLAS and Boost should not been assigned in Makefile" created --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: オープン Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Versions of OpneBLAS and Boost should not been assigned in Makefile -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30207 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30207 From noreply ＠ sourceforge.jp Wed Nov 28 13:47:12 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 28 Nov 2012 13:47:12 +0900 Subject: [Molds-dev] [molds] #30208: Estimate of "Block size" is needed each time that DSYSV is called. Message-ID: <1354078032.584488.6397.nullmailer@sourceforge.jp> #30208: Estimate of "Block size" is needed each time that DSYSV is called. Open Date: 2012-11-28 13:47 Last Update: 2012-11-28 13:47 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30208 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30208 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-28 13:47 Update by: mikiya_fujii * New Ticket "Estimate of "Block size" is needed each time that DSYSV is called." created --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: バグ Status: オープン Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 4 Resolution: なし --------------------------------------------------------------------- Ticket details: "Block size" is needed in each time that DSYSV is called.[[BR]] In Lapack. cc, following sections should be called in each time. {{{ 218 #pragma omp critical 219 { 220 if(!this->calculatedDsysvBlockSize){ 221 lwork = -1; 222 double tempWork[3]={0.0, 0.0, 0.0}; 223 dsysv(&uplo, &size, &nrhs, convertedMatrix, &lda, ipiv, tempB, &ldb, tempWork, &lwork, &info); 224 this->calculatedDsysvBlockSize = true; 225 this->dsysvBlockSize = tempWork[0]/size; 226 } 227 } }}} In, Lapack_GNU.cpp following sections should be called in each time. {{{ 218 #pragma omp critical 219 { 220 if(!this->calculatedDsysvBlockSize){ 221 lwork = -1; 222 double tempWork[3]={0.0, 0.0, 0.0}; 223 info = LAPACKE_dsysv_work(LAPACK_COL_MAJOR, uplo, size, nrhs, convertedMatrix, lda, ipiv, tempB, ldb, tempWork, lwork); 224 this->calculatedDsysvBlockSize = true; 225 this->dsysvBlockSize = tempWork[0]/size; 226 } 227 } }}} -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30208 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30208 From mikiya.fujii ＠ gmail.com Wed Nov 28 14:04:13 2012 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Wed, 28 Nov 2012 14:04:13 +0900 Subject: [Molds-dev] Makefiles are modified!!! Message-ID: Dear all, I commit r1144 for the ticket #30207: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30207. With this commit, you may be not able to compile the MolDS. The reason is that versions of Boost and OpenBLAS are changed to be not assigned in the Makefiles. In such case, please hit following command For intel-compiler $ sudo ln -s "pass to your boost" /usr/local/boost For gcc $ sudo ln -s "pass to your boost" /usr/local/boost $ sudo ln -s "pass to your opneBLAS" /usr/local/openblas My best, Mikiya *************************************** Mikiya Fujii, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: fujii ＠ tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** From noreply ＠ sourceforge.jp Wed Nov 28 14:05:51 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 28 Nov 2012 14:05:51 +0900 Subject: [Molds-dev] [molds] #30207: Versions of OpneBLAS and Boost should not been assigned in Makefile Message-ID: <1354079151.665882.4211.nullmailer@sourceforge.jp> #30207: Versions of OpneBLAS and Boost should not been assigned in Makefile Open Date: 2012-11-28 13:40 Last Update: 2012-11-28 14:05 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30207 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30207 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-28 14:05 Update by: mikiya_fujii * Ticket Close date set to 2012-11-28 14:05 * 状況 Update from オープン to 完了. * 解決法 Update from なし to 修正済み. Comment: fixed at r1144 --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: 完了 Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Versions of OpneBLAS and Boost should not been assigned in Makefile -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30207 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30207 From noreply ＠ sourceforge.jp Wed Nov 28 14:06:52 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 28 Nov 2012 14:06:52 +0900 Subject: [Molds-dev] [molds] #30153: Boltzman-distributor Message-ID: <1354079212.054102.9386.nullmailer@sourceforge.jp> #30153: Boltzman-distributor Open Date: 2012-11-20 01:04 Last Update: 2012-11-28 14:06 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30153 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30153 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-28 14:06 Update by: mikiya_fujii * マイルストーン Update from ver0.2 to (未割り当て). --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: オープン Priority: 5 - 中 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Boltzman-distributor -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30153 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30153 From noreply ＠ sourceforge.jp Wed Nov 28 14:07:09 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 28 Nov 2012 14:07:09 +0900 Subject: [Molds-dev] [molds] #27464: Force calculated twice in RPMD Message-ID: <1354079229.528342.9415.nullmailer@sourceforge.jp> #27464: Force calculated twice in RPMD Open Date: 2012-02-09 15:23 Last Update: 2012-11-28 14:07 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27464 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27464 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-28 14:07 Update by: mikiya_fujii * マイルストーン Update from ver0.2 to (未割り当て). --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: バグ Status: オープン Priority: 5 - 中 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: RPMD::DoRPMD calculates force twice. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27464 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27464 From noreply ＠ sourceforge.jp Wed Nov 28 14:07:40 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 28 Nov 2012 14:07:40 +0900 Subject: [Molds-dev] [molds] #27832: NULL check is carried in debug-build. Message-ID: <1354079260.186930.5302.nullmailer@sourceforge.jp> #27832: NULL check is carried in debug-build. Open Date: 2012-03-14 19:51 Last Update: 2012-11-28 14:07 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27832 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27832 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-28 14:07 Update by: mikiya_fujii * マイルストーン Update from ver0.2 to (未割り当て). --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: オープン Priority: 4 MileStone: (未割り当て) Component: (未割り当て) Severity: 4 Resolution: なし --------------------------------------------------------------------- Ticket details: NULL check is only carried in debug-build. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27832 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27832 From noreply ＠ sourceforge.jp Wed Nov 28 14:07:53 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 28 Nov 2012 14:07:53 +0900 Subject: [Molds-dev] [molds] #26390: Combine with OCTA/GOURMET Message-ID: <1354079273.550946.9475.nullmailer@sourceforge.jp> #26390: Combine with OCTA/GOURMET Open Date: 2011-09-25 23:25 Last Update: 2012-11-28 14:07 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=26390 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=26390 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-28 14:07 Update by: mikiya_fujii * マイルストーン Update from ver0.2 to (未割り当て). --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: オープン Priority: 4 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Combine with OCTA/GOURMET -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=26390 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=26390 From noreply ＠ sourceforge.jp Wed Nov 28 14:08:21 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 28 Nov 2012 14:08:21 +0900 Subject: [Molds-dev] [molds] #27054: Smart pointa Message-ID: <1354079301.839070.6332.nullmailer@sourceforge.jp> #27054: Smart pointa Open Date: 2012-01-05 09:49 Last Update: 2012-11-28 14:08 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27054 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27054 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-28 14:08 Update by: mikiya_fujii * マイルストーン Update from ver0.2 to (未割り当て). --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: オープン Priority: 5 - 中 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Smart pointa for user-defined class. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27054 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27054 From noreply ＠ sourceforge.jp Wed Nov 28 14:08:34 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 28 Nov 2012 14:08:34 +0900 Subject: [Molds-dev] [molds] #27097: Non-adiabtic RPMD Message-ID: <1354079314.614822.6354.nullmailer@sourceforge.jp> #27097: Non-adiabtic RPMD Open Date: 2012-01-10 16:01 Last Update: 2012-11-28 14:08 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27097 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27097 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-28 14:08 Update by: mikiya_fujii * マイルストーン Update from ver0.2 to (未割り当て). --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: オープン Priority: 5 - 中 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Non-adiabtic RPMD -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27097 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27097 From noreply ＠ sourceforge.jp Wed Nov 28 14:08:59 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 28 Nov 2012 14:08:59 +0900 Subject: [Molds-dev] [molds] #26387: wiki(English) Message-ID: <1354079339.266303.6391.nullmailer@sourceforge.jp> #26387: wiki(English) Open Date: 2011-09-25 23:20 Last Update: 2012-11-28 14:08 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=26387 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=26387 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-28 14:08 Update by: mikiya_fujii * マイルストーン Update from ver0.2 to (未割り当て). --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: オープン Priority: 3 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: wiki(English) -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=26387 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=26387 From noreply ＠ sourceforge.jp Thu Nov 29 03:36:05 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 03:36:05 +0900 Subject: [Molds-dev] [molds] #30208: Estimate of "Block size" is needed each time that DSYSV is called. Message-ID: <1354127765.945466.16748.nullmailer@sourceforge.jp> #30208: Estimate of "Block size" is needed each time that DSYSV is called. Open Date: 2012-11-28 13:47 Last Update: 2012-11-29 03:36 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30208 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30208 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 03:36 Update by: mikiya_fujii * Ticket Close date set to 2012-11-29 03:36 * 状況 Update from オープン to 完了. * 解決法 Update from なし to 修正済み. Comment: fixed at r1146. --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: バグ Status: 完了 Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 4 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: "Block size" is needed in each time that DSYSV is called.[[BR]] In Lapack. cc, following sections should be called in each time. {{{ 218 #pragma omp critical 219 { 220 if(!this->calculatedDsysvBlockSize){ 221 lwork = -1; 222 double tempWork[3]={0.0, 0.0, 0.0}; 223 dsysv(&uplo, &size, &nrhs, convertedMatrix, &lda, ipiv, tempB, &ldb, tempWork, &lwork, &info); 224 this->calculatedDsysvBlockSize = true; 225 this->dsysvBlockSize = tempWork[0]/size; 226 } 227 } }}} In, Lapack_GNU.cpp following sections should be called in each time. {{{ 218 #pragma omp critical 219 { 220 if(!this->calculatedDsysvBlockSize){ 221 lwork = -1; 222 double tempWork[3]={0.0, 0.0, 0.0}; 223 info = LAPACKE_dsysv_work(LAPACK_COL_MAJOR, uplo, size, nrhs, convertedMatrix, lda, ipiv, tempB, ldb, tempWork, lwork); 224 this->calculatedDsysvBlockSize = true; 225 this->dsysvBlockSize = tempWork[0]/size; 226 } 227 } }}} -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30208 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30208 From noreply ＠ sourceforge.jp Thu Nov 29 10:25:40 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 10:25:40 +0900 Subject: [Molds-dev] [molds] #30161: overfolw of int in "Lapack.cpp" Message-ID: <1354152340.358386.9290.nullmailer@sourceforge.jp> #30161: overfolw of int in "Lapack.cpp" Open Date: 2012-11-20 17:45 Last Update: 2012-11-29 10:25 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30161 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30161 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 10:25 Update by: mikiya_fujii * Ticket Close date set to 2012-11-29 10:25 * 状況 Update from オープン to 完了. * 解決法 Update from なし to 修正済み. Comment: fixed at r1147 --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: バグ Status: 完了 Priority: 6 MileStone: ver0.2 Component: (未割り当て) Severity: 6 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: overfolw of int in "Lapack.cpp"[[BR]] Type of arguments for size of array should be modified to size_t from int -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30161 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30161 From noreply ＠ sourceforge.jp Thu Nov 29 10:27:35 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 10:27:35 +0900 Subject: [Molds-dev] [molds] #27027: Test for ver0.2 Message-ID: <1354152455.213928.2918.nullmailer@sourceforge.jp> #27027: Test for ver0.2 Open Date: 2011-12-31 16:52 Last Update: 2012-11-29 10:27 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27027 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27027 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 10:27 Update by: mikiya_fujii * Details Updated --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: オープン Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Tests for MO, rotation, translation, principal axes, dipole moments, frequencies, and optimizations. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27027 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27027 From noreply ＠ sourceforge.jp Thu Nov 29 10:37:07 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 10:37:07 +0900 Subject: [Molds-dev] [molds] #27027: Test for ver0.2 Message-ID: <1354153027.828831.4828.nullmailer@sourceforge.jp> #27027: Test for ver0.2 Open Date: 2011-12-31 16:52 Last Update: 2012-11-29 10:37 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27027 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27027 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 10:37 Update by: mikiya_fujii * Details Updated --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: オープン Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Tests for MO, rotation, translation, principal axes, dipole moments, frequencies, optimizations, and other features. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27027 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27027 From noreply ＠ sourceforge.jp Thu Nov 29 10:47:49 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 10:47:49 +0900 Subject: [Molds-dev] [molds] #30216: Delete trunk/benchmark Message-ID: <1354153669.604573.10523.nullmailer@sourceforge.jp> #30216: Delete trunk/benchmark Open Date: 2012-11-29 10:47 Last Update: 2012-11-29 10:47 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30216 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30216 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 10:47 Update by: mikiya_fujii * New Ticket "Delete trunk/benchmark" created --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: バグ Status: オープン Priority: 2 MileStone: ver0.2 Component: (未割り当て) Severity: 2 Resolution: なし --------------------------------------------------------------------- Ticket details: Delete trunk/benchmark because this directory is not used and not updated. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30216 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30216 From noreply ＠ sourceforge.jp Thu Nov 29 10:49:20 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 10:49:20 +0900 Subject: [Molds-dev] [molds] #30216: Delete trunk/benchmark Message-ID: <1354153760.812750.11604.nullmailer@sourceforge.jp> #30216: Delete trunk/benchmark Open Date: 2012-11-29 10:47 Last Update: 2012-11-29 10:49 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30216 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30216 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 10:49 Update by: mikiya_fujii * Ticket Close date set to 2012-11-29 10:49 * 状況 Update from オープン to 完了. * 解決法 Update from なし to 修正済み. Comment: fixed at r1148 --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: バグ Status: 完了 Priority: 2 MileStone: ver0.2 Component: (未割り当て) Severity: 2 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Delete trunk/benchmark because this directory is not used and not updated. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30216 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30216 From noreply ＠ sourceforge.jp Thu Nov 29 10:49:28 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 10:49:28 +0900 Subject: [Molds-dev] [molds] #30216: Delete trunk/benchmark Message-ID: <1354153768.714239.11621.nullmailer@sourceforge.jp> #30216: Delete trunk/benchmark Open Date: 2012-11-29 10:47 Last Update: 2012-11-29 10:49 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30216 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30216 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 10:49 Update by: mikiya_fujii * チケットの種類 Update from バグ to パッチ. --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: 完了 Priority: 2 MileStone: ver0.2 Component: (未割り当て) Severity: 2 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Delete trunk/benchmark because this directory is not used and not updated. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30216 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30216 From noreply ＠ sourceforge.jp Thu Nov 29 10:50:34 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 10:50:34 +0900 Subject: [Molds-dev] [molds] #30217: Update doc/README.txt for ver0.2 Message-ID: <1354153834.840929.23897.nullmailer@sourceforge.jp> #30217: Update doc/README.txt for ver0.2 Open Date: 2012-11-29 10:50 Last Update: 2012-11-29 10:50 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30217 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30217 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 10:50 Update by: mikiya_fujii * New Ticket "Update doc/README.txt for ver0.2" created --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: サポートリクエスト Status: オープン Priority: 5 - 中 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Update doc/README.txt for ver0.2 -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30217 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30217 From noreply ＠ sourceforge.jp Thu Nov 29 10:50:46 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 10:50:46 +0900 Subject: [Molds-dev] [molds] #30217: Update doc/README.txt for ver0.2 Message-ID: <1354153846.299881.12730.nullmailer@sourceforge.jp> #30217: Update doc/README.txt for ver0.2 Open Date: 2012-11-29 10:50 Last Update: 2012-11-29 10:50 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30217 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30217 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 10:50 Update by: mikiya_fujii * マイルストーン Update from (未割り当て) to ver0.2. --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: サポートリクエスト Status: オープン Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Update doc/README.txt for ver0.2 -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30217 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30217 From noreply ＠ sourceforge.jp Thu Nov 29 13:21:18 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 13:21:18 +0900 Subject: [Molds-dev] [molds] #30217: Update doc/README.txt for ver0.2 Message-ID: <1354162878.082380.4903.nullmailer@sourceforge.jp> #30217: Update doc/README.txt for ver0.2 Open Date: 2012-11-29 10:50 Last Update: 2012-11-29 13:21 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30217 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30217 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 13:21 Update by: mikiya_fujii * Ticket Close date set to 2012-11-29 13:21 * 状況 Update from オープン to 完了. * 解決法 Update from なし to 修正済み. Comment: fixed at r1151 --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: サポートリクエスト Status: 完了 Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Update doc/README.txt for ver0.2 -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30217 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30217 From noreply ＠ sourceforge.jp Thu Nov 29 13:21:39 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 13:21:39 +0900 Subject: [Molds-dev] [molds] #28588: automake Message-ID: <1354162899.153942.12143.nullmailer@sourceforge.jp> #28588: automake Open Date: 2012-05-31 10:08 Last Update: 2012-11-29 13:21 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=28588 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=28588 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 13:21 Update by: mikiya_fujii * マイルストーン Update from ver0.2 to (未割り当て). --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: ktns Type: 機能リクエスト Status: オープン Priority: 5 - 中 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Implementation of the automake. Use the branch "http://sourceforge.jp/projects/molds/scm/svn/branches" -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=28588 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=28588 From noreply ＠ sourceforge.jp Thu Nov 29 13:27:04 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 13:27:04 +0900 Subject: [Molds-dev] [molds] #30161: overfolw of int in "Lapack.cpp" Message-ID: <1354163224.077418.4258.nullmailer@sourceforge.jp> #30161: overfolw of int in "Lapack.cpp" Open Date: 2012-11-20 17:45 Last Update: 2012-11-29 13:27 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30161 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30161 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 13:27 Update by: mikiya_fujii * 状況 Update from 完了 to オープン. --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: バグ Status: オープン Priority: 6 MileStone: ver0.2 Component: (未割り当て) Severity: 6 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: overfolw of int in "Lapack.cpp"[[BR]] Type of arguments for size of array should be modified to size_t from int -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30161 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30161 From noreply ＠ sourceforge.jp Thu Nov 29 13:28:03 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 13:28:03 +0900 Subject: [Molds-dev] [molds] #30161: overfolw of int in "Lapack.cpp" Message-ID: <1354163283.188517.16504.nullmailer@sourceforge.jp> #30161: overfolw of int in "Lapack.cpp" Open Date: 2012-11-20 17:45 Last Update: 2012-11-29 13:28 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30161 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30161 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 13:28 Update by: mikiya_fujii Comment: CFLAGS in Makefile is not valid for 32 bits machine in r1151 --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: バグ Status: オープン Priority: 6 MileStone: ver0.2 Component: (未割り当て) Severity: 6 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: overfolw of int in "Lapack.cpp"[[BR]] Type of arguments for size of array should be modified to size_t from int -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30161 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30161 From noreply ＠ sourceforge.jp Thu Nov 29 13:28:43 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 13:28:43 +0900 Subject: [Molds-dev] [molds] #30161: overfolw of int in "Lapack.cpp" Message-ID: <1354163323.398334.16562.nullmailer@sourceforge.jp> #30161: overfolw of int in "Lapack.cpp" Open Date: 2012-11-20 17:45 Last Update: 2012-11-29 13:28 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30161 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30161 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 13:28 Update by: mikiya_fujii Comment: CFLAGS in Makefile is not valid for 32 bits machine in r1151, which is reason of the re-open. --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: バグ Status: オープン Priority: 6 MileStone: ver0.2 Component: (未割り当て) Severity: 6 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: overfolw of int in "Lapack.cpp"[[BR]] Type of arguments for size of array should be modified to size_t from int -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30161 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30161 From noreply ＠ sourceforge.jp Thu Nov 29 13:37:08 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 13:37:08 +0900 Subject: [Molds-dev] [molds] #30161: overfolw of int in "Lapack.cpp" Message-ID: <1354163828.218603.9855.nullmailer@sourceforge.jp> #30161: overfolw of int in "Lapack.cpp" Open Date: 2012-11-20 17:45 Last Update: 2012-11-29 13:37 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30161 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30161 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 13:37 Update by: mikiya_fujii * 状況 Update from オープン to 完了. * Ticket Close date set to 2012-11-29 13:37 Comment: bug related to CFLAGS is fixed in r1152 --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: バグ Status: 完了 Priority: 6 MileStone: ver0.2 Component: (未割り当て) Severity: 6 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: overfolw of int in "Lapack.cpp"[[BR]] Type of arguments for size of array should be modified to size_t from int -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30161 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30161 From noreply ＠ sourceforge.jp Thu Nov 29 18:33:32 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 18:33:32 +0900 Subject: [Molds-dev] [molds] #30218: Make `make depend' needless Message-ID: <1354181612.900479.24138.nullmailer@sourceforge.jp> #30218: Make `make depend' needless Open Date: 2012-11-29 18:33 Last Update: 2012-11-29 18:33 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30218 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30218 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 18:33 Update by: ktns * New Ticket "Make `make depend' needless " created --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: パッチ Status: オープン Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Instead of invoking `make depend; make' in first build, build with only single 'make' command. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30218 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30218 From noreply ＠ sourceforge.jp Thu Nov 29 18:42:13 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 18:42:13 +0900 Subject: [Molds-dev] [molds] #30218: Make `make depend' needless Message-ID: <1354182133.542969.29722.nullmailer@sourceforge.jp> #30218: Make `make depend' needless Open Date: 2012-11-29 18:33 Last Update: 2012-11-29 18:42 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30218 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30218 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 18:42 Update by: ktns * Ticket Close date set to 2012-11-29 18:42 * 状況 Update from オープン to 完了. * 解決法 Update from なし to 修正済み. Comment: Implemented on r1153 But, maybe `make depend' is required after adding some source files into Makefile. --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: パッチ Status: 完了 Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Instead of invoking `make depend; make' in first build, build with only single 'make' command. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30218 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30218 From noreply ＠ sourceforge.jp Thu Nov 29 19:13:47 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 19:13:47 +0900 Subject: [Molds-dev] [molds] #30217: Update doc/README.txt for ver0.2 Message-ID: <1354184027.100376.7250.nullmailer@sourceforge.jp> #30217: Update doc/README.txt for ver0.2 Open Date: 2012-11-29 10:50 Last Update: 2012-11-29 19:13 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30217 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30217 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 19:13 Update by: mikiya_fujii * 状況 Update from 完了 to オープン. * 解決法 Update from 修正済み to なし. Comment: Re-opened for #30218 http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30218 --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: サポートリクエスト Status: オープン Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Update doc/README.txt for ver0.2 -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30217 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30217 From noreply ＠ sourceforge.jp Thu Nov 29 19:21:13 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 19:21:13 +0900 Subject: [Molds-dev] [molds] #27027: Test for ver0.2 Message-ID: <1354184473.690857.12189.nullmailer@sourceforge.jp> #27027: Test for ver0.2 Open Date: 2011-12-31 16:52 Last Update: 2012-11-29 19:21 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27027 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27027 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 19:21 Update by: mikiya_fujii * Ticket Close date set to 2012-11-29 19:21 * 状況 Update from オープン to 完了. * 解決法 Update from なし to 修正済み. Comment: fixed at r1154 --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: 完了 Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Tests for MO, rotation, translation, principal axes, dipole moments, frequencies, optimizations, and other features. -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=27027 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=27027 From noreply ＠ sourceforge.jp Thu Nov 29 19:23:49 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 29 Nov 2012 19:23:49 +0900 Subject: [Molds-dev] [molds] #30217: Update doc/README.txt for ver0.2 Message-ID: <1354184629.689576.9146.nullmailer@sourceforge.jp> #30217: Update doc/README.txt for ver0.2 Open Date: 2012-11-29 10:50 Last Update: 2012-11-29 19:23 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30217 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30217 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-29 19:23 Update by: mikiya_fujii * Ticket Close date set to 2012-11-29 19:23 * 解決法 Update from なし to 修正済み. * 状況 Update from オープン to 完了. Comment: fixed at r1155 --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: サポートリクエスト Status: 完了 Priority: 5 - 中 MileStone: ver0.2 Component: (未割り当て) Severity: 5 - 中 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Update doc/README.txt for ver0.2 -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30217 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30217 From mikiya.fujii ＠ gmail.com Fri Nov 30 04:14:57 2012 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Fri, 30 Nov 2012 04:14:57 +0900 Subject: [Molds-dev] Tagged ver0.2.0! Message-ID: Dear all, I tagged version 0.2.0!!! Let's proceed to the 0.3.0 from today. Mikiya *************************************** Mikiya Fujii, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: fujii ＠ tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** From noreply ＠ sourceforge.jp Fri Nov 30 09:38:28 2012 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Fri, 30 Nov 2012 09:38:28 +0900 Subject: [Molds-dev] [molds] #28791: Semiclassical method (NASCO) Message-ID: <1354235908.628652.21545.nullmailer@sourceforge.jp> #28791: Semiclassical method (NASCO) Open Date: 2012-06-19 17:58 Last Update: 2012-11-30 09:38 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=28791 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=28791 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-11-30 09:38 Update by: mikiya_fujii * マイルストーン Update from (未割り当て) to ver0.3.0. --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: オープン Priority: 5 - 中 MileStone: ver0.3.0 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Semiclassical method (NASCO) -- This is Ticket on Project MolDS. MolDS Project hosted on SourceForge.JP. Project URL: http://sourceforge.jp/projects/molds SourceForge.JP: http://sourceforge.jp URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=28791 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=28791