Commit: 073836f160b7daa917b1f49e41d3d7c82beb2360 - myprojects-hg-reborn (hg)

Commit MetaInfo

• Revision: 073836f160b7daa917b1f49e41d3d7c82beb2360 (tree)
• Time: 2007-10-19 19:47:15
• Author: iselllo
• Commiter: iselllo

Log Message

I added the code mytest_3_particle_kind.tcl which simulates the dynamics
of two particles estabilishing a fene bond when they are close.

Change Summary

• add: TCL-codes/mytest_3_particle_kind.tcl

Incremental Difference

diff -r cf66a6ca9a83 -r 073836f160b7 TCL-codes/mytest_3_particle_kind.tcl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TCL-codes/mytest_3_particle_kind.tcl	Fri Oct 19 10:47:15 2007 +0000
@@ -0,0 +1,170 @@
+set n_part 2; set density 0.0007
+set box_l [expr pow($n_part/$density,1./3.)]
+
+setmd box_l $box_l $box_l $box_l
+setmd periodic 1 1 1
+
+
+inter 0 fene 7.0 4.5 
+# I define here a fene potential
+
+set q 0; set type 0
+
+# I now set the particle charge to 0 and see if the code works the same of not
+
+for {set i 0} { $i < $n_part } {incr i} {
+set posx [expr $box_l*[t_random]]
+set posy [expr $box_l*[t_random]]
+set posz [expr $box_l*[t_random]]
+part $i pos $posx $posy $posz q $q type $type
+}
+
+
+puts "[part ]"
+
+setmd time_step 0.01; setmd skin 0.4
+set temp 0.0005; set gamma 0.01
+thermostat langevin $temp $gamma
+
+
+
+
+
+set sig 1.0; set cut [expr 1.12246*$sig]
+set eps 1.0; set shift [expr 0.25*$eps]
+#inter 0 0 lennard-jones $eps $sig $cut $shift 0
+#inter 0 0  morse 1000. 0.01 1. 1.3
+
+
+#probably the warm-up is now useless since there is no lennard-jones potential
+
+
+
+
+
+
+
+set integ_steps 200
+
+for {set cap 20} {$cap < 200} {incr cap 20} {
+puts "t=[setmd time] E=[analyze energy total]"
+inter ljforcecap $cap; integrate $integ_steps
+set min [analyze mindist]
+
+}
+
+puts "Warmup finished. Minimal distance now $min"
+#uncap forces
+inter ljforcecap 0
+
+puts "end of equilibration"
+
+set vmd "yes"
+
+if { $vmd == "yes" } {
+# This calls a small tcl script which starts the program    #
+# VMD and opens a socket connection between ESPResSo and    #
+# VMD.                                                      #
+    prepare_vmd_connection tutorial 3000
+
+# Just wait a moment until VMD has started.                 #
+# The 'exec' command is quite useful since with that you can#
+# call any other program from within your simulation script.#
+    exec sleep 4
+
+# The additional command imd steers the socket connection   #
+# to VMD, e.g. sending the actual coordinates               #
+    imd positions
+}
+
+
+#prepare the saving of the results
+
+#set obs [open "rg_lorenzo.dat" "w"] 
+
+
+proc and {a b} {return [expr $a && $b]}
+
+set activate_fene 1
+set fene_warning 1
+set integ_step 20
+
+for {set i 0} { $i < 2000 } { incr i} {
+set temp [expr [analyze energy kinetic]/(1.5*$n_part)]
+#puts "t=[setmd time] E=[analyze energy total], T=$temp"
+integrate $integ_steps
+
+# puts "save configuration"
+
+
+#puts "[analyze nbhood 1 2.]"
+
+
+set acti [analyze nbhood 1 4.5]
+
+
+#puts "acti is, $acti"
+set myfene [llength $acti]
+if {$myfene > 1 && $fene_warning == 1} {
+puts "the particles are within the FENE range"
+set fene_warning 0
+}
+
+set neighbor [analyze nbhood 1 2.]
+set mylen [llength $neighbor]
+#puts "mylen is, $mylen"
+
+if { $mylen == 2 && $activate_fene == 1 } {
+part 0 bond 0 1
+puts "activated fene bond!"
+set activate_fene 0
+}
+#part 0 bond 0 1
+#set activate_fene 0
+
+
+
+
+set f [open "config_$i" "w"]
+blockfile $f write tclvariable {box_l density}
+blockfile $f write variable box_l
+blockfile $f write particles {id pos type}
+close $f
+# if you have turned on the vmd option you can now
+    # follow what your simulation is doing
+    if { $vmd == "yes" } { imd positions }
+
+#Now I calculate the radius of gyration
+# set rg [lindex [analyze rg] 0]
+#puts $obs "[setmd time] $rg"
+
+}
+
+
+
+
+
+#close $obs
+puts "end of integration" 
+
+#plotObs "rg.dat" { 1:2 } labels { "time" "rg" } out "rg"
+#exec gv rg.ps
+
+set f [open "config_1" "r"]
+while { [blockfile $f read auto] != "eof" } {}
+close $f
+
+puts "ok reading the block file"
+
+set rdf [analyze rdf 0 0 0.9 [expr $box_l/2] 100]
+set rlist ""
+set rdflist ""
+foreach value [lindex $rdf 1] {
+lappend rlist [lindex $value 0]
+lappend rdflist [lindex $value 1]
+}
+
+
+
+
+puts "So far so good"
\ No newline at end of file