From okymmolds ＠ gmail.com Fri Jan 4 00:15:49 2013 From: okymmolds ＠ gmail.com (Okuyama) Date: Fri, 04 Jan 2013 00:15:49 +0900 Subject: [Molds-dev] [Patch] Unpaired_electron_population Message-ID: <50E5A0A5.6040606@gmail.com> Dear colleagues This is Okuyama. I send patch files to impliment the unpaired electron population (UEP) and the input control to this mailing list. The patch files are the following files: *calc_uep_without_opt_ctrl.patch *add_opt_ctrl.patch calc_uep_without_opt_ctrl.patch adds source code to be available the unpaired electron population. By appling this patch file, it's possible to calculate the unpaired electron population of excited states on each single atom in molecule. Upto this implimentation, you can calculate the unpaired electron population of nth-excited states by adding the follwing input: CIS mulliken n END Next, the file, add_opt_ctrl.patch adds the input control of the unpaired electron population. The input control executes the calculation of the UEP when there is a keyword, 'unpaired_electron_population' in the CIS input. *Procedure to apply the patch files to the MolDS Revision of the Molds is 1234 In a directory, trunk, 1. patch -p0 < calc_uep_without_opt_ctrl.patch 2. patch -p2 < add_opt_ctrl.patch *How to use the UEP calculation Example) Calculation of the UEP of the m and n-th excited states CIS .... mulliken m mulliken n unpaired_electron_population .... END I have made sure the following terms: * There are not segmentation fault and abort by executing all the test inputs. * The MolDS.out is created by executing make depend INTEL=64 && make INTEL=64 * For all the test inputs including CIS keyword, I added the follwing keyword: CIS .... mulliken 2 mulliken 3 unpaired_electron_population ... END Under above condition, I make sure that there is no segmentation fault. At last, in this implimentation, it will not calculate the UEP at the ground state. The reason why the UEP at the ground state is zero and, therefore this calculation is nonsense. Best regards. -------------- next part -------------- $B%F%-%9%H7A<00J30$NE:IU%U%!%$%k$rJ]4I$7$^$7$?(B... $B%U%!%$%kL>(B: calc_uep_without_opt_ctrl.patch $B7?(B: text/x-patch $B%5%$%:(B: 8604 $B%P%$%H(B $B ＠ bL@(B: $BL5$7(B URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20130104/ce956b15/attachment.bin -------------- next part -------------- $B%F%-%9%H7A<00J30$NE:IU%U%!%$%k$rJ]4I$7$^$7$?(B... $B%U%!%$%kL>(B: add_opt_ctrl.patch $B7?(B: text/x-patch $B%5%$%:(B: 4357 $B%P%$%H(B $B ＠ bL@(B: $BL5$7(B URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20130104/ce956b15/attachment-0001.bin From mikiya.fujii ＠ gmail.com Sun Jan 6 01:55:57 2013 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Sun, 6 Jan 2013 01:55:57 +0900 Subject: [Molds-dev] Fwd: [molds] #30409: Integrate Blas/Lapack_GNU.cpp In-Reply-To: <1356758653.273423.6775.nullmailer@sourceforge.jp> References: <1356758653.273423.6775.nullmailer@sourceforge.jp> Message-ID: Dear ktns, Nice work! M *************************************** 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: 2012/12/29 Subject: [Molds-dev] [molds] #30409: Integrate Blas/Lapack_GNU.cpp To: SourceForge Ticket System #30409: Integrate Blas/Lapack_GNU.cpp Open Date: 2012-12-29 13:28 Last Update: 2012-12-29 14:24 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30409 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30409 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2012-12-29 14:24 Update by: ktns * Ticket Close date set to 2012-12-29 14:24 * 状況 Update from オープン to 完了. * 解決法 Update from なし to 修正済み. Comment: Done by r1220 --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: パッチ Status: 完了 Priority: 4 MileStone: (未割り当て) Component: (未割り当て) Severity: 4 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Integrate Blas/Lapack_GNU.cpp into Blas/Lapack.cpp using #if directive. -- 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=30409 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30409 _______________________________________________ MolDS-dev mailing list MolDS-dev ＠ lists.sourceforge.jp http://lists.sourceforge.jp/mailman/listinfo/molds-dev From mikiya.fujii ＠ gmail.com Sun Jan 6 02:55:54 2013 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Sun, 6 Jan 2013 02:55:54 +0900 Subject: [Molds-dev] [Patch] Unpaired_electron_population In-Reply-To: <50E5A0A5.6040606@gmail.com> References: <50E5A0A5.6040606@gmail.com> Message-ID: Dear Okuyama, Thanks for your patches. I had reviewed them. *** Your coding-grammar and -style are quite fine! But, I ask you to fix only one modification about input control: (1) UEP should be set as "unpaired_electron_population yes" in CIS-directive, that is, the following input obeys the MolDS's input style. CIS .... mulliken m mulliken n unpaired_electron_population yes .... END The corresponding code in the InputParser.cpp (r1234 which your 2 patches and my modification had been applied to) is written as 742 int InputParser::ParseConditionsCIS(vector* inputTerms, int parseIndex) const{ 743 Parameters::GetInstance()->SetRequiresCIS(true); 744 parseIndex++; . . . . 827 // unpaired electron population 828 if((*inputTerms)[parseIndex].compare(this->stringCISUnpairedPop) == 0){ 829 if((*inputTerms)[parseIndex+1].compare(this->stringYES) == 0){ 830 Parameters::GetInstance()->SetRequiresUnpairedPopCIS(true); 831 } 832 else{ 833 Parameters::GetInstance()->SetRequiresUnpairedPopCIS(false); 834 } 835 parseIndex++; 836 } 837 parseIndex++; 838 } 839 return parseIndex; 840 } With integration of the (1) to your second patch "add_opt_ctrl.patch", please commit your code to the trunk. *** Besides, I ask you to do two more tasks about this ticket. [1] Update test input and output files in the molds/trunk/test for the UEP. I think that updating of only "c2h6_pm3_directCIS_singlet.in" and "c2h6_pm3_directCIS_singlet.dat" is enough. [2] Update documents (molds/trunk/doc/README.txt) to use UEP. Explanation of the UEP option should be written in the -paragraph of the README.txt. Of course, please commit [1] and [2] too. Please ask me if you have any question. 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/ *************************************** 2013/1/4 Okuyama : > Dear colleagues > > This is Okuyama. > > I send patch files to impliment the unpaired electron population (UEP) > and the input control to this mailing list. > The patch files are the following files: > *calc_uep_without_opt_ctrl.patch > *add_opt_ctrl.patch > > calc_uep_without_opt_ctrl.patch adds source code to be available the > unpaired electron population. > By appling this patch file, it's possible to calculate the unpaired > electron population of excited states on each single atom in molecule. > Upto this implimentation, you can calculate the unpaired electron > population of nth-excited states > by adding the follwing input: > CIS > mulliken n > END > Next, the file, add_opt_ctrl.patch adds the input control of the > unpaired electron population. > The input control executes the calculation of the UEP > when there is a keyword, 'unpaired_electron_population' in the CIS input. > > *Procedure to apply the patch files to the MolDS > Revision of the Molds is 1234 > In a directory, trunk, > 1. patch -p0 < calc_uep_without_opt_ctrl.patch > 2. patch -p2 < add_opt_ctrl.patch > > *How to use the UEP calculation > Example) Calculation of the UEP of the m and n-th excited states > CIS > .... > mulliken m > mulliken n > unpaired_electron_population > .... > END > > I have made sure the following terms: > * There are not segmentation fault and abort by executing all the > test inputs. > * The MolDS.out is created by executing make depend INTEL=64 && > make INTEL=64 > * For all the test inputs including CIS keyword, I added the > follwing keyword: > CIS > .... > mulliken 2 > mulliken 3 > unpaired_electron_population > ... > END > Under above condition, I make sure that there is no segmentation > fault. > > At last, in this implimentation, it will not calculate the UEP at the > ground state. > The reason why the UEP at the ground state is zero and, therefore this > calculation is nonsense. > > Best regards. > > -------------- 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: calc_uep_without_opt_ctrl.patch > 型: text/x-patch > サイズ: 8604 バイト > 説明: 無し > URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20130104/ce956b15/attachment.bin > -------------- 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: add_opt_ctrl.patch > 型: text/x-patch > サイズ: 4357 バイト > 説明: 無し > URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20130104/ce956b15/attachment-0001.bin > _______________________________________________ > MolDS-dev mailing list > MolDS-dev ＠ lists.sourceforge.jp > http://lists.sourceforge.jp/mailman/listinfo/molds-dev From okymmolds ＠ gmail.com Tue Jan 8 00:01:33 2013 From: okymmolds ＠ gmail.com (Okuyama) Date: Tue, 08 Jan 2013 00:01:33 +0900 Subject: [Molds-dev] [Patch] Unpaired_electron_population In-Reply-To: References: <50E5A0A5.6040606@gmail.com> Message-ID: <50EAE34D.5050502@gmail.com> Dear Mr. Fujii, This is Okuyama. Thanks for reviewing my patch files. I read your E-mail. In your E-mail, I think there is a problem in the source code that you suggested. You suggested new source code: 742 int InputParser::ParseConditionsCIS(vector* inputTerms, int parseIndex) const{ 743 Parameters::GetInstance()->SetRequiresCIS(true); 744 parseIndex++; . . . . 827 // unpaired electron population 828 if((*inputTerms)[parseIndex].compare(this->stringCISUnpairedPop) == 0){ 829 if((*inputTerms)[parseIndex+1].compare(this->stringYES) == 0){ 830 Parameters::GetInstance()->SetRequiresUnpairedPopCIS(true); 831 } 832 else{ 833 Parameters::GetInstance()->SetRequiresUnpairedPopCIS(false); 834 } 835 parseIndex++; 836 } 837 parseIndex++; 838 } 839 return parseIndex; 840 } I implement the above source code into my source code and run the implemented source code in my PC. In CIS input, the following input is OK: unpaired_electron_population yes or unpaired_electron_population no However, the calculation stops abnormaly (segmentation fault) when the following input: unpaired_electron_population Now, I'm investigating the problem. I may have any time to solve this problem since I can't solve the problem.... I think I'd like to have a chance to talk with you by mobile phone etc. Best regards. Okuyama On 2013年01月06日 02:55, Mikiya Fujii wrote: > Dear Okuyama, > > Thanks for your patches. I had reviewed them. > > *** > Your coding-grammar and -style are quite fine! > But, I ask you to fix only one modification about input control: > (1) UEP should be set as "unpaired_electron_population yes" in CIS-directive, > that is, the following input obeys the MolDS's input style. > > CIS > .... > mulliken m > mulliken n > unpaired_electron_population yes > .... > END > > The corresponding code in the InputParser.cpp (r1234 which your 2 > patches and my modification had been applied to) is written as > > 742 int InputParser::ParseConditionsCIS(vector* > inputTerms, int parseIndex) const{ > 743 Parameters::GetInstance()->SetRequiresCIS(true); > 744 parseIndex++; > . > . > . > . > 827 // unpaired electron population > 828 if((*inputTerms)[parseIndex].compare(this->stringCISUnpairedPop) > == 0){ > 829 if((*inputTerms)[parseIndex+1].compare(this->stringYES) == 0){ > 830 Parameters::GetInstance()->SetRequiresUnpairedPopCIS(true); > 831 } > 832 else{ > 833 Parameters::GetInstance()->SetRequiresUnpairedPopCIS(false); > 834 } > 835 parseIndex++; > 836 } > 837 parseIndex++; > 838 } > 839 return parseIndex; > 840 } > > With integration of the (1) to your second patch "add_opt_ctrl.patch", > please commit your code to the trunk. > > > *** > Besides, I ask you to do two more tasks about this ticket. > [1] Update test input and output files in the molds/trunk/test for the UEP. > I think that updating of only "c2h6_pm3_directCIS_singlet.in" and > "c2h6_pm3_directCIS_singlet.dat" is enough. > [2] Update documents (molds/trunk/doc/README.txt) to use UEP. > Explanation of the UEP option should be written in the > -paragraph of the README.txt. > > Of course, please commit [1] and [2] too. > > > Please ask me if you have any question. > 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/ > *************************************** > > > 2013/1/4 Okuyama : >> Dear colleagues >> >> This is Okuyama. >> >> I send patch files to impliment the unpaired electron population (UEP) >> and the input control to this mailing list. >> The patch files are the following files: >> *calc_uep_without_opt_ctrl.patch >> *add_opt_ctrl.patch >> >> calc_uep_without_opt_ctrl.patch adds source code to be available the >> unpaired electron population. >> By appling this patch file, it's possible to calculate the unpaired >> electron population of excited states on each single atom in molecule. >> Upto this implimentation, you can calculate the unpaired electron >> population of nth-excited states >> by adding the follwing input: >> CIS >> mulliken n >> END >> Next, the file, add_opt_ctrl.patch adds the input control of the >> unpaired electron population. >> The input control executes the calculation of the UEP >> when there is a keyword, 'unpaired_electron_population' in the CIS input. >> >> *Procedure to apply the patch files to the MolDS >> Revision of the Molds is 1234 >> In a directory, trunk, >> 1. patch -p0 < calc_uep_without_opt_ctrl.patch >> 2. patch -p2 < add_opt_ctrl.patch >> >> *How to use the UEP calculation >> Example) Calculation of the UEP of the m and n-th excited states >> CIS >> .... >> mulliken m >> mulliken n >> unpaired_electron_population >> .... >> END >> >> I have made sure the following terms: >> * There are not segmentation fault and abort by executing all the >> test inputs. >> * The MolDS.out is created by executing make depend INTEL=64 && >> make INTEL=64 >> * For all the test inputs including CIS keyword, I added the >> follwing keyword: >> CIS >> .... >> mulliken 2 >> mulliken 3 >> unpaired_electron_population >> ... >> END >> Under above condition, I make sure that there is no segmentation >> fault. >> >> At last, in this implimentation, it will not calculate the UEP at the >> ground state. >> The reason why the UEP at the ground state is zero and, therefore this >> calculation is nonsense. >> >> Best regards. >> >> -------------- 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: calc_uep_without_opt_ctrl.patch >> 型: text/x-patch >> サイズ: 8604 バイト >> 説明: 無し >> URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20130104/ce956b15/attachment.bin >> -------------- 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: add_opt_ctrl.patch >> 型: text/x-patch >> サイズ: 4357 バイト >> 説明: 無し >> URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20130104/ce956b15/attachment-0001.bin >> _______________________________________________ >> MolDS-dev mailing list >> MolDS-dev ＠ lists.sourceforge.jp >> http://lists.sourceforge.jp/mailman/listinfo/molds-dev From noreply ＠ sourceforge.jp Mon Jan 21 18:12:02 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Mon, 21 Jan 2013 18:12:02 +0900 Subject: [Molds-dev] [molds] #30554: Output on/off of DIIS and "eMax" Message-ID: <1358759522.643511.24111.nullmailer@sourceforge.jp> #30554: Output on/off of DIIS and "eMax" Open Date: 2013-01-21 18:12 Last Update: 2013-01-21 18:12 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30554 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30554 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-21 18:12 Update by: mikiya_fujii * New Ticket "Output on/off of DIIS and "eMax" " 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: ver0.3.0 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Output on/off of DIIS and "eMax" of Cndo2::DoDIIS for each SCF step. -- 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=30554 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30554 From noreply ＠ sourceforge.jp Tue Jan 22 03:45:30 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 22 Jan 2013 03:45:30 +0900 Subject: [Molds-dev] [molds] #30557: Use boost::math::factorial Message-ID: <1358793930.557859.25382.nullmailer@sourceforge.jp> #30557: Use boost::math::factorial Open Date: 2013-01-22 03:45 Last Update: 2013-01-22 03:45 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30557 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30557 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-22 03:45 Update by: ktns * New Ticket "Use boost::math::factorial" 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: 4 Resolution: なし --------------------------------------------------------------------- Ticket details: Call boost::math::factorial in MolDS_base::Factorial. -- 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=30557 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30557 From noreply ＠ sourceforge.jp Tue Jan 22 05:46:08 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 22 Jan 2013 05:46:08 +0900 Subject: [Molds-dev] [molds] #30557: Use boost::math::factorial Message-ID: <1358801168.139653.25170.nullmailer@sourceforge.jp> #30557: Use boost::math::factorial Open Date: 2013-01-22 03:45 Last Update: 2013-01-22 05:46 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30557 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30557 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-22 05:46 Update by: ktns * 解決法 Update from なし to 修正済み. --------------------------------------------------------------------- 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: 4 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Call boost::math::factorial in MolDS_base::Factorial. -- 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=30557 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30557 From noreply ＠ sourceforge.jp Tue Jan 22 15:56:04 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 22 Jan 2013 15:56:04 +0900 Subject: [Molds-dev] [molds] #30560: Use dsyrk in CalcOrbitalElectronPopulation Message-ID: <1358837764.052286.11116.nullmailer@sourceforge.jp> #30560: Use dsyrk in CalcOrbitalElectronPopulation Open Date: 2013-01-22 15:56 Last Update: 2013-01-22 15:56 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30560 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30560 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-22 15:56 Update by: ktns * New Ticket "Use dsyrk in CalcOrbitalElectronPopulation" created --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: パッチ 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: Speed up CalcOrbitalElectronPopulation by dsyrk routine of BLAS. Below is a part of a gprof output at r1238 {{{ Flat profile: Each sample counts as 0.01 seconds. % cumulative self self total time seconds seconds calls Ks/call Ks/call name 58.42 7105.98 7105.98 657 0.01 0.01 MolDS_cndo::Cndo2::CalcOrbitalElectronPopulation(double**, MolDS_base::Molecule const&, double const* const*) const 7.65 8036.59 930.61 655 0.00 0.00 MolDS_cndo::Cndo2::DoDIIS(double**, double const* const*, double***, double***, double**, double*, int, MolDS_base::Molecule c onst&, int) const 5.89 8752.62 716.03 158880184 0.00 0.00 MolDS_mndo::Mndo::GetFockOffDiagElement(MolDS_base_atoms::Atom const&, MolDS_base_atoms::Atom const&, int, int, int, int, Mol DS_base::Molecule const&, double const* const*, double const* const*, double const* const*, double const* const* const* const* const* const*, bool) const 4.89 9346.98 594.36 pow.A ... }}} -- 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=30560 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30560 From mikiya.fujii ＠ gmail.com Tue Jan 22 16:26:30 2013 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Tue, 22 Jan 2013 16:26:30 +0900 Subject: [Molds-dev] [molds] #30560: Use dsyrk in CalcOrbitalElectronPopulation In-Reply-To: <1358837764.052286.11116.nullmailer@sourceforge.jp> References: <1358837764.052286.11116.nullmailer@sourceforge.jp> Message-ID: Dear ktns, Thanks for the interesting profile. Can you attach the input used for this profile to this ticket page ? http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30560 If unpublished data is included, you should not attach the input !!! My bset *************************************** 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/ *************************************** 2013/1/22 SourceForge Ticket System : > #30560: Use dsyrk in CalcOrbitalElectronPopulation > > Open Date: 2013-01-22 15:56 > Last Update: 2013-01-22 15:56 > > URL for this Ticket: > http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30560 > RSS feed for this Ticket: > http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30560 > > --------------------------------------------------------------------- > > Last Changes/Comment for this Ticket: > 2013-01-22 15:56 Update by: ktns > > * New Ticket "Use dsyrk in CalcOrbitalElectronPopulation" created > > --------------------------------------------------------------------- > Ticket Status: > > Reporter: ktns > Owner: ktns > Type: パッチ > 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: > > Speed up CalcOrbitalElectronPopulation by dsyrk routine of BLAS. > > Below is a part of a gprof output at r1238 > {{{ > Flat profile: > > Each sample counts as 0.01 seconds. > % cumulative self self total > time seconds seconds calls Ks/call Ks/call name > 58.42 7105.98 7105.98 657 0.01 0.01 MolDS_cndo::Cndo2::CalcOrbitalElectronPopulation(double**, MolDS_base::Molecule const&, double const* const*) const > 7.65 8036.59 930.61 655 0.00 0.00 MolDS_cndo::Cndo2::DoDIIS(double**, double const* const*, double***, double***, double**, double*, int, MolDS_base::Molecule c > onst&, int) const > 5.89 8752.62 716.03 158880184 0.00 0.00 MolDS_mndo::Mndo::GetFockOffDiagElement(MolDS_base_atoms::Atom const&, MolDS_base_atoms::Atom const&, int, int, int, int, Mol > DS_base::Molecule const&, double const* const*, double const* const*, double const* const*, double const* const* const* const* const* const*, bool) const > 4.89 9346.98 594.36 pow.A > ... > }}} > > > -- > 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=30560 > RSS feed for this Ticket: > http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30560 > > _______________________________________________ > MolDS-dev mailing list > MolDS-dev ＠ lists.sourceforge.jp > http://lists.sourceforge.jp/mailman/listinfo/molds-dev From noreply ＠ sourceforge.jp Tue Jan 22 19:06:07 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 22 Jan 2013 19:06:07 +0900 Subject: [Molds-dev] [molds] #30562: Add dsyrk routine into BLAS wrapper Message-ID: <1358849167.312682.16996.nullmailer@sourceforge.jp> #30562: Add dsyrk routine into BLAS wrapper Open Date: 2013-01-22 19:06 Last Update: 2013-01-22 19:06 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30562 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30562 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-22 19:06 Update by: ktns * New Ticket "Add dsyrk routine into BLAS wrapper" created --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: パッチ 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: Add a wrapper function for dsyrk routine into BLAS wrapper. -- 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=30562 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30562 From ktns.87 ＠ gmail.com Tue Jan 22 19:37:06 2013 From: ktns.87 ＠ gmail.com (Katsuhiko Nishimra) Date: Tue, 22 Jan 2013 19:37:06 +0900 Subject: [Molds-dev] Fwd: [molds] #30560: Use dsyrk in CalcOrbitalElectronPopulation In-Reply-To: References: <1358837764.052286.11116.nullmailer@sourceforge.jp> Message-ID: Dear Mr. Fujii, I'm sorry, but the input does include unpublished data, and I have already edited the file so it's gone. My best, 2013/1/22 Mikiya Fujii > Dear ktns, > > Thanks for the interesting profile. > Can you attach the input used for this profile to this ticket page ? > http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30560 > > If unpublished data is included, you should not attach the input !!! > > > My bset > > > *************************************** > 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/ > *************************************** > > > 2013/1/22 SourceForge Ticket System : > > #30560: Use dsyrk in CalcOrbitalElectronPopulation > > > > Open Date: 2013-01-22 15:56 > > Last Update: 2013-01-22 15:56 > > > > URL for this Ticket: > > http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30560 > > RSS feed for this Ticket: > > http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30560 > > > > --------------------------------------------------------------------- > > > > Last Changes/Comment for this Ticket: > > 2013-01-22 15:56 Update by: ktns > > > > * New Ticket "Use dsyrk in CalcOrbitalElectronPopulation" created > > > > --------------------------------------------------------------------- > > Ticket Status: > > > > Reporter: ktns > > Owner: ktns > > Type: パッチ > > 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: > > > > Speed up CalcOrbitalElectronPopulation by dsyrk routine of BLAS. > > > > Below is a part of a gprof output at r1238 > > {{{ > > Flat profile: > > > > Each sample counts as 0.01 seconds. > > % cumulative self self total > > time seconds seconds calls Ks/call Ks/call name > > 58.42 7105.98 7105.98 657 0.01 0.01 > MolDS_cndo::Cndo2::CalcOrbitalElectronPopulation(double**, > MolDS_base::Molecule const&, double const* const*) const > > 7.65 8036.59 930.61 655 0.00 0.00 > MolDS_cndo::Cndo2::DoDIIS(double**, double const* const*, double***, > double***, double**, double*, int, MolDS_base::Molecule c > > onst&, int) const > > 5.89 8752.62 716.03 158880184 0.00 0.00 > MolDS_mndo::Mndo::GetFockOffDiagElement(MolDS_base_atoms::Atom const&, > MolDS_base_atoms::Atom const&, int, int, int, int, Mol > > DS_base::Molecule const&, double const* const*, double const* const*, > double const* const*, double const* const* const* const* const* const*, > bool) const > > 4.89 9346.98 594.36 pow.A > > ... > > }}} > > > > > > -- > > 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=30560 > > RSS feed for this Ticket: > > http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30560 > > > > _______________________________________________ > > 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 > -- Katsuhiko Nishimra ktns.87 ＠ gmail.com -------------- next part -------------- HTML$B$NE:IU%U%!%$%k$rJ]4I$7$^$7$?(B... URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20130122/9d6a47d4/attachment.htm From noreply ＠ sourceforge.jp Wed Jan 23 07:15:00 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 23 Jan 2013 07:15:00 +0900 Subject: [Molds-dev] [molds] #30554: Output on/off of DIIS and "eMax" Message-ID: <1358892900.001109.31723.nullmailer@sourceforge.jp> #30554: Output on/off of DIIS and "eMax" Open Date: 2013-01-21 18:12 Last Update: 2013-01-23 07:14 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30554 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30554 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-23 07:14 Update by: mikiya_fujii * Ticket Close date set to 2013-01-23 07:14 * 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 r1246 . The "eMax" was renamed to "diisError" in Cndo2::DoDIIS. --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: 完了 Priority: 5 - 中 MileStone: ver0.3.0 Component: (未割り当て) Severity: 5 - 中 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Output on/off of DIIS and "eMax" of Cndo2::DoDIIS for each SCF step. -- 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=30554 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30554 From noreply ＠ sourceforge.jp Wed Jan 23 15:47:47 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 23 Jan 2013 15:47:47 +0900 Subject: [Molds-dev] [molds] #30566: Use cblas routines only in BLAS wrapper Message-ID: <1358923667.749749.29423.nullmailer@sourceforge.jp> #30566: Use cblas routines only in BLAS wrapper Open Date: 2013-01-23 15:47 Last Update: 2013-01-23 15:47 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30566 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30566 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-23 15:47 Update by: ktns * New Ticket "Use cblas routines only in BLAS wrapper" created --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: (未割り当て) 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: Use cblas routines even if mkl is used. -- 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=30566 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30566 From noreply ＠ sourceforge.jp Wed Jan 23 19:42:12 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 23 Jan 2013 19:42:12 +0900 Subject: [Molds-dev] [molds] #30566: Use cblas routines only in BLAS wrapper Message-ID: <1358937732.796304.11847.nullmailer@sourceforge.jp> #30566: Use cblas routines only in BLAS wrapper Open Date: 2013-01-23 15:47 Last Update: 2013-01-23 19:42 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30566 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30566 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-23 19:42 Update by: ktns * 担当者 Update from (未割り当て) to ktns. --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns 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: Use cblas routines even if mkl is used. -- 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=30566 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30566 From noreply ＠ sourceforge.jp Thu Jan 24 19:54:17 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 24 Jan 2013 19:54:17 +0900 Subject: [Molds-dev] [molds] #30582: LDFLAGS from environment variable Message-ID: <1359024857.589618.7317.nullmailer@sourceforge.jp> #30582: LDFLAGS from environment variable Open Date: 2013-01-24 19:54 Last Update: 2013-01-24 19:54 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30582 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30582 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-24 19:54 Update by: ktns * New Ticket "LDFLAGS from environment variable" created --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: サポートリクエスト Status: オープン Priority: 2 MileStone: (未割り当て) Component: (未割り当て) Severity: 2 Resolution: なし --------------------------------------------------------------------- Ticket details: Allow user to build with additional LDFLAGS as below. {{{ make INTEL=64 LDFLAGS='-g -pg' }}} -- 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=30582 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30582 From noreply ＠ sourceforge.jp Thu Jan 24 19:55:50 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 24 Jan 2013 19:55:50 +0900 Subject: [Molds-dev] [molds] #30583: CFLAGS from environment variable Message-ID: <1359024950.158016.7451.nullmailer@sourceforge.jp> #30583: CFLAGS from environment variable Open Date: 2013-01-24 19:55 Last Update: 2013-01-24 19:55 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30583 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30583 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-24 19:55 Update by: ktns * New Ticket "CFLAGS from environment variable" created --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: サポートリクエスト Status: オープン Priority: 2 MileStone: (未割り当て) Component: (未割り当て) Severity: 2 Resolution: なし --------------------------------------------------------------------- Ticket details: Allow user to build with additional CFLAGS as below. {{{ make INTEL=64 CFLAGS='-g -pg' }}} -- 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=30583 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30583 From noreply ＠ sourceforge.jp Thu Jan 24 20:46:53 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 24 Jan 2013 20:46:53 +0900 Subject: [Molds-dev] [molds] #30218: Make `make depend' needless Message-ID: <1359028013.786639.24121.nullmailer@sourceforge.jp> #30218: Make `make depend' needless Open Date: 2012-11-29 18:33 Last Update: 2013-01-24 20:46 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: 2013-01-24 20:46 Update by: ktns * 状況 Update from 完了 to オープン. * Details Updated * マイルストーン Update from ver0.2 (完了済) to (未割り当て). --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns 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: 修正済み --------------------------------------------------------------------- Ticket details: Instead of invoking {{{ make depend make }}} on 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 Jan 24 21:11:08 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 24 Jan 2013 21:11:08 +0900 Subject: [Molds-dev] [molds] #30218: Make `make depend' needless Message-ID: <1359029468.894394.20908.nullmailer@sourceforge.jp> #30218: Make `make depend' needless Open Date: 2012-11-29 18:33 Last Update: 2013-01-24 21:11 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: 2013-01-24 21:11 Update by: ktns * Ticket Close date set to 2013-01-24 21:11 * 状況 Update from オープン to 完了. Comment: Fixed the code not to generate objfile.dep every time after source code change on r1250 --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: パッチ Status: 完了 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: Instead of invoking {{{ make depend make }}} on 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 Jan 24 23:06:20 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 24 Jan 2013 23:06:20 +0900 Subject: [Molds-dev] [molds] #30584: Change working directory to the test directory at the first of the test script Message-ID: <1359036380.634738.12255.nullmailer@sourceforge.jp> #30584: Change working directory to the test directory at the first of the test script Open Date: 2013-01-24 23:06 Last Update: 2013-01-24 23:06 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30584 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30584 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-24 23:06 Update by: ktns * New Ticket "Change working directory to the test directory at the first of the test script" created --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: サポートリクエスト Status: オープン Priority: 2 MileStone: (未割り当て) Component: (未割り当て) Severity: 2 Resolution: なし --------------------------------------------------------------------- Ticket details: Change working directory to the test directory at the first of the test script to allow one to execute the test script at the src directory or others. -- 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=30584 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30584 From noreply ＠ sourceforge.jp Thu Jan 24 23:12:13 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 24 Jan 2013 23:12:13 +0900 Subject: [Molds-dev] [molds] #30584: Change working directory to the test directory at the first of the test script Message-ID: <1359036733.164685.20965.nullmailer@sourceforge.jp> #30584: Change working directory to the test directory at the first of the test script Open Date: 2013-01-24 23:06 Last Update: 2013-01-24 23:12 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30584 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30584 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-24 23:12 Update by: ktns * Ticket Close date set to 2013-01-24 23:12 * 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 at r1253 --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: サポートリクエスト Status: 完了 Priority: 2 MileStone: (未割り当て) Component: (未割り当て) Severity: 2 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Change working directory to the test directory at the first of the test script to allow one to execute the test script at the src directory or others. -- 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=30584 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30584 From noreply ＠ sourceforge.jp Thu Jan 24 23:46:45 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Thu, 24 Jan 2013 23:46:45 +0900 Subject: [Molds-dev] [molds] #30218: Make `make depend' needless Message-ID: <1359038805.196895.24428.nullmailer@sourceforge.jp> #30218: Make `make depend' needless Open Date: 2012-11-29 18:33 Last Update: 2013-01-24 23:46 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: 2013-01-24 23:46 Update by: ktns Comment: r1254 makes {{{ make depend }}} command to forcibly generates the dependency file. --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: パッチ Status: 完了 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: Instead of invoking {{{ make depend make }}} on 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 Fri Jan 25 03:48:20 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Fri, 25 Jan 2013 03:48:20 +0900 Subject: [Molds-dev] [molds] #30560: Use dsyrk in CalcOrbitalElectronPopulation Message-ID: <1359053300.261488.14582.nullmailer@sourceforge.jp> #30560: Use dsyrk in CalcOrbitalElectronPopulation Open Date: 2013-01-22 15:56 Last Update: 2013-01-25 03:48 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30560 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30560 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-25 03:48 Update by: ktns * Ticket Close date set to 2013-01-25 03:48 * 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 at r1256 --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: パッチ Status: 完了 Priority: 4 MileStone: (未割り当て) Component: (未割り当て) Severity: 5 - 中 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Speed up CalcOrbitalElectronPopulation by dsyrk routine of BLAS. Below is a part of a gprof output at r1238 {{{ Flat profile: Each sample counts as 0.01 seconds. % cumulative self self total time seconds seconds calls Ks/call Ks/call name 58.42 7105.98 7105.98 657 0.01 0.01 MolDS_cndo::Cndo2::CalcOrbitalElectronPopulation(double**, MolDS_base::Molecule const&, double const* const*) const 7.65 8036.59 930.61 655 0.00 0.00 MolDS_cndo::Cndo2::DoDIIS(double**, double const* const*, double***, double***, double**, double*, int, MolDS_base::Molecule c onst&, int) const 5.89 8752.62 716.03 158880184 0.00 0.00 MolDS_mndo::Mndo::GetFockOffDiagElement(MolDS_base_atoms::Atom const&, MolDS_base_atoms::Atom const&, int, int, int, int, Mol DS_base::Molecule const&, double const* const*, double const* const*, double const* const*, double const* const* const* const* const* const*, bool) const 4.89 9346.98 594.36 pow.A ... }}} -- 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=30560 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30560 From noreply ＠ sourceforge.jp Fri Jan 25 16:53:06 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Fri, 25 Jan 2013 16:53:06 +0900 Subject: [Molds-dev] [molds] #30566: Use cblas routines only in BLAS wrapper Message-ID: <1359100386.735253.32208.nullmailer@sourceforge.jp> #30566: Use cblas routines only in BLAS wrapper Open Date: 2013-01-23 15:47 Last Update: 2013-01-25 16:53 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30566 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30566 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-25 16:53 Update by: ktns Comment: Implemented in trunk at r1249. --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns 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: Use cblas routines even if mkl is used. -- 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=30566 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30566 From noreply ＠ sourceforge.jp Fri Jan 25 16:54:51 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Fri, 25 Jan 2013 16:54:51 +0900 Subject: [Molds-dev] [molds] #30566: Use cblas routines only in BLAS wrapper Message-ID: <1359100491.535488.843.nullmailer@sourceforge.jp> #30566: Use cblas routines only in BLAS wrapper Open Date: 2013-01-23 15:47 Last Update: 2013-01-25 16:54 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30566 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30566 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-25 16:54 Update by: ktns * Ticket Close date set to 2013-01-25 16:54 * 状況 Update from オープン to 完了. Comment: Implemented in automake branch at r1259 --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: ktns Type: パッチ Status: 完了 Priority: 4 MileStone: (未割り当て) Component: (未割り当て) Severity: 4 Resolution: なし --------------------------------------------------------------------- Ticket details: Use cblas routines even if mkl is used. -- 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=30566 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30566 From noreply ＠ sourceforge.jp Sat Jan 26 04:29:10 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Sat, 26 Jan 2013 04:29:10 +0900 Subject: [Molds-dev] [molds] #30595: Abort with independent DIIS equations Message-ID: <1359142150.766532.12688.nullmailer@sourceforge.jp> #30595: Abort with independent DIIS equations Open Date: 2013-01-26 04:29 Last Update: 2013-01-26 04:29 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30595 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30595 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-26 04:29 Update by: ktns * New Ticket "Abort with independent DIIS equations" created --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: (未割り当て) Type: バグ Status: オープン Priority: 6 MileStone: (未割り当て) Component: (未割り当て) Severity: 6 Resolution: なし --------------------------------------------------------------------- Ticket details: Program abnormally exits when DIIS equations are independent with an error as follows. {{{ Error in wrappers::Lapack::Dsysv: info != 0: info = 5 }}} -- 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=30595 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30595 From noreply ＠ sourceforge.jp Sat Jan 26 07:13:55 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Sat, 26 Jan 2013 07:13:55 +0900 Subject: [Molds-dev] [molds] #30596: Speed up Mndo::CalcMatrix Message-ID: <1359152035.195699.12816.nullmailer@sourceforge.jp> #30596: Speed up Mndo::CalcMatrix Open Date: 2013-01-26 07:13 Last Update: 2013-01-26 07:13 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30596 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30596 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-26 07:13 Update by: mikiya_fujii * New Ticket "Speed up Mndo::CalcMatrix" 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: ver0.3.0 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Speed up Mndo::CalcMatrix -- 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=30596 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30596 From noreply ＠ sourceforge.jp Sat Jan 26 07:17:35 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Sat, 26 Jan 2013 07:17:35 +0900 Subject: [Molds-dev] [molds] #30596: Speed up Mndo::CalcCISMatrix Message-ID: <1359152255.494472.3520.nullmailer@sourceforge.jp> #30596: Speed up Mndo::CalcCISMatrix Open Date: 2013-01-26 07:13 Last Update: 2013-01-26 07:17 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30596 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30596 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-26 07:17 Update by: mikiya_fujii * Summary 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: ver0.3.0 Component: (未割り当て) Severity: 5 - 中 Resolution: なし --------------------------------------------------------------------- Ticket details: Speed up Mndo::CalcMatrix -- 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=30596 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30596 From noreply ＠ sourceforge.jp Sat Jan 26 07:24:54 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Sat, 26 Jan 2013 07:24:54 +0900 Subject: [Molds-dev] [molds] #30596: Speed up Mndo::CalcCISMatrix Message-ID: <1359152694.948028.26047.nullmailer@sourceforge.jp> #30596: Speed up Mndo::CalcCISMatrix Open Date: 2013-01-26 07:13 Last Update: 2013-01-26 07:24 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30596 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30596 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-26 07:24 Update by: mikiya_fujii * Ticket Close date set to 2013-01-26 07:24 * 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 r1262 --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: 機能リクエスト Status: 完了 Priority: 5 - 中 MileStone: ver0.3.0 Component: (未割り当て) Severity: 5 - 中 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Speed up Mndo::CalcMatrix -- 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=30596 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30596 From noreply ＠ sourceforge.jp Sun Jan 27 09:32:37 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Sun, 27 Jan 2013 09:32:37 +0900 Subject: [Molds-dev] [molds] #30605: RMS density change is not RMS Message-ID: <1359246757.671069.26034.nullmailer@sourceforge.jp> #30605: RMS density change is not RMS Open Date: 2013-01-27 09:32 Last Update: 2013-01-27 09:32 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30605 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30605 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-27 09:32 Update by: ktns * New Ticket "RMS density change is not RMS" created --------------------------------------------------------------------- Ticket Status: Reporter: ktns Owner: (未割り当て) Type: バグ Status: オープン Priority: 5 - 中 MileStone: (未割り当て) Component: (未割り当て) Severity: 7 Resolution: なし --------------------------------------------------------------------- Ticket details: RMS density change is not implemented as a root MEAN square. -- 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=30605 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30605 From okymmolds ＠ gmail.com Sun Jan 27 15:26:48 2013 From: okymmolds ＠ gmail.com (Okuyama) Date: Sun, 27 Jan 2013 15:26:48 +0900 Subject: [Molds-dev] On the manual and test input about the UEP Message-ID: <5104C8A8.3010504@gmail.com> Dear Mr. Fujii, I'm going to regist the following terms to a new revision (more than 1262) of the molDS, ■trunk/doc/README.txt Adding the manual of the unpaired electron population to the ■trunk/test/c2h6_pm3_directCIS_singlet.in Adding a option, "unapired_electron_population yes" to a input, "test/c2h6_pm3_directCIS_singlet.in" ■trunk/test/test/c2h6_pm3_directCIS_singlet.dat Replacing a original file(rev. 1262), "test/c2h6_pm3_directCIS_singlet.dat" to a log file that is calculated by the above input. Before doing the registration, I made a patch file that include the above modification. Are my modifications correct? I would like you to give some opinions and a judgement with respect to my modification. P.S.: This patch is based on a revision 1262 of the molDS. How to apply a patch: In trunk, execute the following command, patch -p0 < (The path of this patch file) Best regards. M. Okuyama. -------------- next part -------------- $B%F%-%9%H7A<00J30$NE:IU%U%!%$%k$rJ]4I$7$^$7$?(B... $B%U%!%$%kL>(B: add_uep_doc_and_test.patch $B7?(B: text/x-patch $B%5%$%:(B: 8485 $B%P%$%H(B $B ＠ bL@(B: $BL5$7(B URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20130127/9cdefbc7/attachment.bin From mikiya.fujii ＠ gmail.com Sun Jan 27 19:16:52 2013 From: mikiya.fujii ＠ gmail.com (Mikiya Fujii) Date: Sun, 27 Jan 2013 19:16:52 +0900 Subject: [Molds-dev] On the manual and test input about the UEP In-Reply-To: <5104C8A8.3010504@gmail.com> References: <5104C8A8.3010504@gmail.com> Message-ID: Dear Michihiro, Fine! your coding is basically fine! I request small three modifications (line number is ones after your patch was applied.): (1) Line 280 of doc/README.txt: -"mulliken", and "num_print_coefficients" are prepared as options. +"mulliken", "unpaired_electron_population", and "num_print_coefficients" are prepared as options. 277 -options 278 "davidson", "active_occ", "active_vir", "max_iter", "max_dim", "norm_tol", 279 "nstates", "exciton_energies", "all_transition_dipole_moments", 280- "mulliken", and "num_print_coefficients" are prepared as options. 280+ "mulliken", "unpaired_electron_population", and "num_print_coefficients" are prepared as options. (2) Your comments about UEP in doc/README.txt (line 329 - 334) are moved to between the comments of "mulliken" and "num_print_coefficients" (3) Indent of line 347: 336 E.g. 337 CIS 338 davidson no 339 active_occ 2 340 active_vir 2 341 nstates 1000 342 max_iter 100 343 max_dim 100 344 norm_tol 0.000001 345 mulliken 1 346 mulliken 2 347- unpaired_electron_population yes 347+ unpaired_electron_population yes 348 CIS_END To check above modifications, apply the attached patch instead of your patch to trunk of revision 1262: patch -p0 < (The path to my patch file) 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/ *************************************** 2013/1/27 Okuyama : > Dear Mr. Fujii, > > I'm going to regist the following terms to a new revision (more than > 1262) of the molDS, > > ■trunk/doc/README.txt > Adding the manual of the unpaired electron population to the > ■trunk/test/c2h6_pm3_directCIS_singlet.in > Adding a option, "unapired_electron_population yes" to a input, > "test/c2h6_pm3_directCIS_singlet.in" > ■trunk/test/test/c2h6_pm3_directCIS_singlet.dat > Replacing a original file(rev. 1262), > "test/c2h6_pm3_directCIS_singlet.dat" to a log file > that is calculated by the above input. > > Before doing the registration, I made a patch file that include the > above modification. > Are my modifications correct? > > I would like you to give some opinions and a judgement with respect to > my modification. > > P.S.: This patch is based on a revision 1262 of the molDS. > How to apply a patch: > In trunk, execute the following command, > patch -p0 < (The path of this patch file) > > Best regards. > > M. Okuyama. > -------------- 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: add_uep_doc_and_test.patch > 型: text/x-patch > サイズ: 8485 バイト > 説明: 無し > URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20130127/9cdefbc7/attachment.bin > _______________________________________________ > MolDS-dev mailing list > MolDS-dev ＠ lists.sourceforge.jp > http://lists.sourceforge.jp/mailman/listinfo/molds-dev -------------- 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: unpairMF.patch 型: application/octet-stream サイズ: 8888 バイト 説明: 無し URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20130127/833a9a85/attachment.obj From okymmolds ＠ gmail.com Sun Jan 27 20:18:58 2013 From: okymmolds ＠ gmail.com (Okuyama) Date: Sun, 27 Jan 2013 20:18:58 +0900 Subject: [Molds-dev] On the manual and test input about the UEP In-Reply-To: References: <5104C8A8.3010504@gmail.com> Message-ID: <51050D22.8020103@gmail.com> Dear Mr. Fujii Thanks for sending your opinions and encouragements!! I make sure your modification by applying your patch, 'unpairMF.patch'. So, I think that the source code which applied your patch and your modifcation are consistent. Next, I think that I will try to commit the source code by appling your patch, 'unpairMF.patch'. Can I commit the source code? M. Okuyama Best regards. On 2013年01月27日 19:16, Mikiya Fujii wrote: > Dear Michihiro, > > Fine! your coding is basically fine! > I request small three modifications (line number is ones after your > patch was applied.): > > (1) Line 280 of doc/README.txt: > -"mulliken", and "num_print_coefficients" are prepared as options. > +"mulliken", "unpaired_electron_population", and > "num_print_coefficients" are prepared as options. > 277 -options > 278 "davidson", "active_occ", "active_vir", "max_iter", > "max_dim", "norm_tol", > 279 "nstates", "exciton_energies", "all_transition_dipole_moments", > 280- "mulliken", and "num_print_coefficients" are prepared as options. > 280+ "mulliken", "unpaired_electron_population", and > "num_print_coefficients" are prepared as options. > > (2) Your comments about UEP in doc/README.txt (line 329 - 334) are moved to > between the comments of "mulliken" and "num_print_coefficients" > > (3) Indent of line 347: > > 336 E.g. > 337 CIS > 338 davidson no > 339 active_occ 2 > 340 active_vir 2 > 341 nstates 1000 > 342 max_iter 100 > 343 max_dim 100 > 344 norm_tol 0.000001 > 345 mulliken 1 > 346 mulliken 2 > 347- unpaired_electron_population yes > 347+ unpaired_electron_population yes > 348 CIS_END > > > To check above modifications, apply the attached patch instead of your > patch to trunk of revision 1262: > patch -p0 < (The path to my patch file) > > 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/ > *************************************** > > > 2013/1/27 Okuyama : >> Dear Mr. Fujii, >> >> I'm going to regist the following terms to a new revision (more than >> 1262) of the molDS, >> >> ■trunk/doc/README.txt >> Adding the manual of the unpaired electron population to the >> ■trunk/test/c2h6_pm3_directCIS_singlet.in >> Adding a option, "unapired_electron_population yes" to a input, >> "test/c2h6_pm3_directCIS_singlet.in" >> ■trunk/test/test/c2h6_pm3_directCIS_singlet.dat >> Replacing a original file(rev. 1262), >> "test/c2h6_pm3_directCIS_singlet.dat" to a log file >> that is calculated by the above input. >> >> Before doing the registration, I made a patch file that include the >> above modification. >> Are my modifications correct? >> >> I would like you to give some opinions and a judgement with respect to >> my modification. >> >> P.S.: This patch is based on a revision 1262 of the molDS. >> How to apply a patch: >> In trunk, execute the following command, >> patch -p0 < (The path of this patch file) >> >> Best regards. >> >> M. Okuyama. >> -------------- 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: add_uep_doc_and_test.patch >> 型: text/x-patch >> サイズ: 8485 バイト >> 説明: 無し >> URL: http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20130127/9cdefbc7/attachment.bin >> _______________________________________________ >> MolDS-dev mailing list >> MolDS-dev ＠ lists.sourceforge.jp >> http://lists.sourceforge.jp/mailman/listinfo/molds-dev From noreply ＠ sourceforge.jp Sun Jan 27 20:59:45 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Sun, 27 Jan 2013 20:59:45 +0900 Subject: [Molds-dev] [molds] #29958: Unpaired electron population at Mulliken type Message-ID: <1359287985.461281.26594.nullmailer@sourceforge.jp> #29958: Unpaired electron population at Mulliken type Open Date: 2012-10-27 03:11 Last Update: 2013-01-27 20:59 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=29958 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=29958 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-27 20:59 Update by: okymmolds Comment: In #1263, the manual and test-input about unpaired electron population in the README.txt and c2h6_pm3_directCIS_singlet.in are added. In this revision, the development of the unpaired electron population is closed. --------------------------------------------------------------------- Ticket Status: Reporter: okymmolds Owner: okymmolds 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: 3 Resolution: なし --------------------------------------------------------------------- Ticket details: Unpaired electron population of a single atom at Mulliken type is developed. Theoret. Chim. Acta (Berl) 48, 175, (1978) Chem. Phys. Lett., 330, 161, (2000). Chem. Phys. Lett., 372, 508, (2003) -- 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=29958 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=29958 From noreply ＠ sourceforge.jp Sun Jan 27 21:00:01 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Sun, 27 Jan 2013 21:00:01 +0900 Subject: [Molds-dev] [molds] #29958: Unpaired electron population at Mulliken type Message-ID: <1359288001.860102.26971.nullmailer@sourceforge.jp> #29958: Unpaired electron population at Mulliken type Open Date: 2012-10-27 03:11 Last Update: 2013-01-27 21:00 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=29958 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=29958 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-27 21:00 Update by: okymmolds * Ticket Close date set to 2013-01-27 21:00 * 状況 Update from オープン to 完了. --------------------------------------------------------------------- Ticket Status: Reporter: okymmolds Owner: okymmolds 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: 3 Resolution: なし --------------------------------------------------------------------- Ticket details: Unpaired electron population of a single atom at Mulliken type is developed. Theoret. Chim. Acta (Berl) 48, 175, (1978) Chem. Phys. Lett., 330, 161, (2000). Chem. Phys. Lett., 372, 508, (2003) -- 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=29958 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=29958 From noreply ＠ sourceforge.jp Tue Jan 29 06:42:22 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 29 Jan 2013 06:42:22 +0900 Subject: [Molds-dev] [molds] #30617: Refactoring how to calculate dipole moments Message-ID: <1359409342.713667.22211.nullmailer@sourceforge.jp> #30617: Refactoring how to calculate dipole moments Open Date: 2013-01-29 06:42 Last Update: 2013-01-29 06:42 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30617 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30617 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-29 06:42 Update by: mikiya_fujii * New Ticket "Refactoring how to calculate dipole moments" created --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ 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: Refactoring how to calculate dipole moments to speed up -- 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=30617 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30617 From noreply ＠ sourceforge.jp Tue Jan 29 06:44:20 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 29 Jan 2013 06:44:20 +0900 Subject: [Molds-dev] [molds] #30617: Refactoring how to calculate dipole moments Message-ID: <1359409460.007035.32037.nullmailer@sourceforge.jp> #30617: Refactoring how to calculate dipole moments Open Date: 2013-01-29 06:42 Last Update: 2013-01-29 06:44 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30617 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30617 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-29 06:44 Update by: mikiya_fujii * Ticket Close date set to 2013-01-29 06:44 * 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 r1264 --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: 完了 Priority: 5 - 中 MileStone: ver0.3.0 Component: (未割り当て) Severity: 5 - 中 Resolution: 修正済み --------------------------------------------------------------------- Ticket details: Refactoring how to calculate dipole moments to speed up -- 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=30617 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30617 From noreply ＠ sourceforge.jp Tue Jan 29 11:54:36 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 29 Jan 2013 11:54:36 +0900 Subject: [Molds-dev] [molds] #30618: Cache totalNumberAOs in each method to speed up Message-ID: <1359428076.469196.7889.nullmailer@sourceforge.jp> #30618: Cache totalNumberAOs in each method to speed up Open Date: 2013-01-29 11:54 Last Update: 2013-01-29 11:54 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30618 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30618 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-29 11:54 Update by: mikiya_fujii * New Ticket "Cache totalNumberAOs in each method to speed up" created --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: バグ 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: Cache totalNumberAOs in each method to speed up. The name of the cached value should be "totalNumberAOs". -- 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=30618 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30618 From noreply ＠ sourceforge.jp Tue Jan 29 14:26:02 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 29 Jan 2013 14:26:02 +0900 Subject: [Molds-dev] [molds] #30621: Inline expand for small methods Message-ID: <1359437162.007007.7868.nullmailer@sourceforge.jp> #30621: Inline expand for small methods Open Date: 2013-01-29 14:26 Last Update: 2013-01-29 14:26 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30621 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30621 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-29 14:26 Update by: mikiya_fujii * New Ticket "Inline expand for small methods" created --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ 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: The following coding-rule is applied:[[BR]] * Methods written within three lines should be inline-expanded explicitly. * Methods written with four more lines can be explicitly inline-expanded for efficiency. -- 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=30621 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30621 From noreply ＠ sourceforge.jp Tue Jan 29 14:26:47 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 29 Jan 2013 14:26:47 +0900 Subject: [Molds-dev] [molds] #30618: Cache totalNumberAOs in each method to speed up Message-ID: <1359437207.922897.8118.nullmailer@sourceforge.jp> #30618: Cache totalNumberAOs in each method to speed up Open Date: 2013-01-29 11:54 Last Update: 2013-01-29 14:26 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30618 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30618 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-29 14:26 Update by: mikiya_fujii * Ticket Close date set to 2013-01-29 14:26 * 状況 Update from オープン to 完了. * 解決法 Update from なし to 直さない. * チケットの種類 Update from バグ to パッチ. Comment: Instead of caching, inline-expand is used. See #30621 . http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30621#preview --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: 完了 Priority: 5 - 中 MileStone: ver0.3.0 Component: (未割り当て) Severity: 5 - 中 Resolution: 直さない --------------------------------------------------------------------- Ticket details: Cache totalNumberAOs in each method to speed up. The name of the cached value should be "totalNumberAOs". -- 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=30618 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30618 From noreply ＠ sourceforge.jp Tue Jan 29 14:29:03 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 29 Jan 2013 14:29:03 +0900 Subject: [Molds-dev] [molds] #27832: NULL check is carried in debug-build. Message-ID: <1359437343.223940.9256.nullmailer@sourceforge.jp> #27832: NULL check is carried in debug-build. Open Date: 2012-03-14 19:51 Last Update: 2013-01-29 14:29 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: 2013-01-29 14:29 Update by: mikiya_fujii * マイルストーン Update from (未割り当て) to ver0.3.0. Comment: For debugging code like checking of NULL pointa references, {{{ #ifdef MOLDS_DBG #endif }}} should used --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: オープン Priority: 4 MileStone: ver0.3.0 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 Tue Jan 29 15:42:57 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 29 Jan 2013 15:42:57 +0900 Subject: [Molds-dev] [molds] #27832: NULL check is carried in debug-build. Message-ID: <1359441777.048195.18661.nullmailer@sourceforge.jp> #27832: NULL check is carried in debug-build. Open Date: 2012-03-14 19:51 Last Update: 2013-01-29 15:42 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: 2013-01-29 15:42 Update by: mikiya_fujii * Ticket Close date set to 2013-01-29 15:42 * 状況 Update from オープン to 完了. * 解決法 Update from なし to 修正済み. Comment: fixed at r1265 --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: 完了 Priority: 4 MileStone: ver0.3.0 Component: (未割り当て) Severity: 4 Resolution: 修正済み --------------------------------------------------------------------- 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 Tue Jan 29 23:13:16 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 29 Jan 2013 23:13:16 +0900 Subject: [Molds-dev] [molds] #30617: Refactoring how to calculate dipole moments Message-ID: <1359468796.620913.12967.nullmailer@sourceforge.jp> #30617: Refactoring how to calculate dipole moments Open Date: 2013-01-29 06:42 Last Update: 2013-01-29 23:13 URL for this Ticket: http://sourceforge.jp/ticket/browse.php?group_id=6231&tid=30617 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30617 --------------------------------------------------------------------- Last Changes/Comment for this Ticket: 2013-01-29 23:13 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. --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ 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: Refactoring how to calculate dipole moments to speed up -- 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=30617 RSS feed for this Ticket: http://sourceforge.jp/ticket/ticket_rss.php?group_id=6231&tid=30617 From noreply ＠ sourceforge.jp Tue Jan 29 23:41:52 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Tue, 29 Jan 2013 23:41:52 +0900 Subject: [Molds-dev] [molds] #27832: NULL check is carried in debug-build. Message-ID: <1359470512.129861.29148.nullmailer@sourceforge.jp> #27832: NULL check is carried in debug-build. Open Date: 2012-03-14 19:51 Last Update: 2013-01-29 23:41 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: 2013-01-29 23:41 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. --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: オープン Priority: 4 MileStone: ver0.3.0 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 Jan 30 00:03:25 2013 From: noreply ＠ sourceforge.jp (SourceForge Ticket System) Date: Wed, 30 Jan 2013 00:03:25 +0900 Subject: [Molds-dev] [molds] #27832: NULL check is carried in debug-build. Message-ID: <1359471805.051840.17508.nullmailer@sourceforge.jp> #27832: NULL check is carried in debug-build. Open Date: 2012-03-14 19:51 Last Update: 2013-01-30 00:03 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: 2013-01-30 00:03 Update by: mikiya_fujii * 解決法 Update from なし to 修正済み. * 状況 Update from オープン to 完了. * Ticket Close date set to 2013-01-30 00:03 Comment: some bugs are fixed at r1266 --------------------------------------------------------------------- Ticket Status: Reporter: mikiya_fujii Owner: mikiya_fujii Type: パッチ Status: 完了 Priority: 4 MileStone: ver0.3.0 Component: (未割り当て) Severity: 4 Resolution: 修正済み --------------------------------------------------------------------- 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