提交: 9e91fa3006a3c1cb4a7a8989966bac6d422a68fe - myprojects-hg-reborn (hg)

Commit MetaInfo

• 修訂: 9e91fa3006a3c1cb4a7a8989966bac6d422a68fe (tree)
• 時間: 2007-11-19 21:29:56
• 作者: iselllo
• Commiter: iselllo

Log Message

I modified mytest_1_particle_kind.tcl (cleaned up a bit the code, but
not 100% sure of what I did...in case revert to the previous version to
find out what happened) and added test.tcl, which evolves and saves some
statistics for a set of Brownian particles.

Change Summary

• modified: TCL-codes/mytest_1_particle_kind.tcl
• add: TCL-codes/test.tcl

差異

diff -r 138006e4acd4 -r 9e91fa3006a3 TCL-codes/mytest_1_particle_kind.tcl
--- a/TCL-codes/mytest_1_particle_kind.tcl	Sat Nov 10 00:39:51 2007 +0000
+++ b/TCL-codes/mytest_1_particle_kind.tcl	Mon Nov 19 12:29:56 2007 +0000
@@ -1,4 +1,4 @@
-set n_part 50; set density 0.02
+set n_part 50; set density 0.06
 set box_l [expr pow($n_part/$density,1./3.)]
 
 
@@ -21,7 +21,7 @@
 }
 
 setmd time_step 0.01; setmd skin 0.4
-set temp 0.01; set gamma  0.25
+set temp 0.02; set gamma  0.25
 thermostat langevin $temp $gamma
 
 
@@ -31,7 +31,7 @@
 #set sig 1.0; set cut [expr 1.12246*$sig]
 #set eps 1.0; set shift [expr 0.25*$eps]
 
-set sig 1.0
+set sig 0.1
 set cut 2.
 set eps 10.
 set shift 0.

diff -r 138006e4acd4 -r 9e91fa3006a3 TCL-codes/test.tcl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TCL-codes/test.tcl	Mon Nov 19 12:29:56 2007 +0000
@@ -0,0 +1,214 @@
+set n_part 2000; #set density 0.00002
+#set box_l [expr pow($n_part/$density,1./3.)]
+
+set box_l 2000.
+set volume [expr pow($box_l,3.)]
+
+set density [expr $n_part/$volume ]
+
+puts "the density is, $density"
+
+
+set magnification 1.
+
+setmd box_l [expr $magnification*$box_l] [expr $magnification*$box_l] [expr $magnification*$box_l]
+setmd periodic 1 1 1
+
+puts "the box side is, $box_l"
+
+
+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]]
+
+set posx [expr $box_l/2.]
+set posy [expr $box_l/2.]
+set posz [expr $box_l/2.]
+
+
+part $i pos $posx $posy $posz q $q type $type
+}
+
+
+
+
+set tot_time 200.
+
+
+set my_step 1.
+
+
+set N_step [expr $tot_time/$my_step]
+
+set N_step [expr round($N_step)]
+
+
+set integ_steps 1
+
+
+
+
+puts "the total number of time steps is, $N_step"
+
+
+setmd time_step $my_step; setmd skin 0.4
+set temp 0.1 ; set gamma  0.1
+thermostat langevin $temp $gamma
+
+
+
+
+
+set sig 1.0
+set cut 20.
+set eps 0.
+set shift 0.
+
+#inter 0 0 lennard-jones $eps $sig $cut $shift 0
+
+
+set tau_increase 10.
+
+set delta_t [expr $integ_steps*$my_step]
+
+puts "delta_t is, $delta_t"
+
+set cap_ini 20.
+set cap_fin 200.
+set delta_cap [expr $cap_fin-$cap_ini]
+set lin_coeff [expr $delta_cap/$tau_increase]
+
+set n_iter_cap [expr $tau_increase/$delta_t]
+
+set n_iter_cap [expr round($n_iter_cap)]
+
+puts "the number of iterations while ramping the potential is, $n_iter_cap"
+
+
+puts "delta_cap is, $delta_cap"
+
+set cap $cap_ini
+
+
+
+
+#for {set i 0} { $i <= $n_iter_cap } { incr i} {
+#puts "t=[setmd time] E=[analyze energy total]"
+#inter ljforcecap $cap; integrate $integ_steps
+
+#set cap  [expr $cap + $lin_coeff*$delta_t ]
+
+#set min [analyze mindist]
+
+#}
+
+#puts "Warmup finished. Minimal distance now $min"
+#uncap forces
+inter ljforcecap 0
+
+puts "end of equilibration"
+
+set vmd "no"
+
+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 "temp.dat" "w"]
+set obs2 [open "tot_energy.dat" "w"]
+#set obs3 [open "aggregation.dat" "w"]
+set obs3 [open "rgyr.dat" "w"] 
+
+set obs4 [open "part_pos.dat" "w"] 
+
+
+set integ_step 20
+
+
+#puts "the simulation time now is, [setmd time]"
+
+# for {set i 0} { $i < 3000 } { incr i} {
+for {set i 0} { $i < $N_step } { incr i $integ_steps} {
+
+set temp [expr [analyze energy kinetic]/(1.5*$n_part)]
+puts "t=[setmd time] "
+
+
+set energy [lindex [analyze energy total] 0]
+puts $obs "[setmd time] $temp"
+
+puts $obs2 "[setmd time] $energy"
+
+
+
+integrate $integ_steps
+
+#puts "save configuration, [part ]"
+part 0 print pos
+set f [open "config_$i" "w"]
+blockfile $f write tclvariable {box_l density}
+blockfile $f write variable box_l
+blockfile $f write particles {pos}
+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 $obs3 "[setmd time] $rg"
+
+puts $obs4 "[setmd time] [part 0 print pos]"
+
+}
+
+#close $obs
+
+
+puts "end of integration" 
+
+
+puts "the simulation time now is, [setmd time]"
+
+#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"