Commit ac481dd5 authored by Dr. Bogdan Tanygin's avatar Dr. Bogdan Tanygin Committed by GitHub

Merge pull request #145 from espressomd/python

Espresso head merge
parents 6ab6af86 272a3612
#############################################################
# #
# Diamond Hydrogel Networks #
# #
#############################################################
# Copyright (C) 2010,2012,2013,2014,2015,2016 The ESPResSo project
# Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
# Max-Planck-Institute for Polymer Research, Theory Group
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ESPResSo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
puts " "
puts "==================================================="
puts "= diamond.tcl ="
puts "==================================================="
puts " "
puts "Program Information: \n[code_info]\n"
#############################################################
# Parameters #
#############################################################
# System identification:
set name "diamond"
set ident "_t6"
# On 'yes' connects to 'vmd' visualizing current configuration
set vmd_output "no"
# System parameters
#############################################################
set N_node 8
set N_P 16
set MPC 20
set N_CI 328
set N_T [expr $N_node + $N_P*$MPC + $N_CI]
set packing { 0.45 0.4 0.1 0.05 0.025 0.01 0.0075 0.005 0.0025 0.001 0.00075 }
# Interaction parameters
#############################################################
# repulsive Lennard Jones
set lj1_eps 1.0
set lj1_sig 1.0
set lj1_cut 1.122462048309373
set lj1_shift [expr -4.0*$lj1_eps*(pow($lj1_cut,-12)-pow($lj1_cut,-6))]
# attractive FENE
set fene_k 15.551
set fene_r 1.25
# electrostatics
set bjerrum 1.75241
set accuracy 1.0e-1
# Integration parameters
#############################################################
setmd time_step 0.012
setmd skin 0.4
thermostat langevin 1.0 1.0
# warmup integration (with capped LJ potential) until particles are at least $min_dist apart (but at least $min_loop loops)
set warm_step 200
set warm_loop 300
set warm_cap1 10
set warm_incr 25
set min_dist 0.9
set min_loop 200
# integration (with full LJ potential) for $int_time
set int_step 1000
set int_time [expr 20000*[setmd time_step]]
# Other parameters
#############################################################
set tcl_precision 6
set random_seeds { }
#############################################################
# Setup System #
#############################################################
if { [file exists "$name$ident.DHN"] } {
set DHN_file [open "$name$ident.DHN" "a"]
} else {
set DHN_file [open "$name$ident.DHN" "w"]
puts -nonewline $DHN_file "ID int_time pack_i density a_cube re rg rh re2/rg2 Temp mindist "
if { $bjerrum > 0.0 } {
puts $DHN_file "p_total D(p_total) p_FENE D(p_FENE) p_lj D(p_lj) p_c D(p_c) p_ideal p_osmotic"
} else { puts $DHN_file "p_total D(p_total) p_FENE D(p_FENE) p_lj D(p_lj) p_ideal p_osmotic" }
flush $DHN_file
}
# Random number generator setup
#############################################################
if { [llength $random_seeds] > 0 } { eval t_random seed $random_seeds }
# Particle & interaction setup
#############################################################
set i 1
foreach pack_i $packing {
set n_p_i $N_P;
set mpc_i $MPC;
set int_time_i $int_time;
set int_step_i $int_step
set n_part $N_T
set name_i "$name[format %02d $i]"
set density [expr $pack_i*(6/[PI])]
set a_cube [expr pow($N_T/$density,1./3.)]
setmd box_l $a_cube $a_cube $a_cube
set bond_l [expr sqrt(3*[sqr [expr $a_cube/4.]])/($mpc_i+1)]
puts "\n====================\n=== System [format %2d $i]/[llength $packing] ===\n===================="
puts "\nSimulate a Diamond Hydrogel Network with $N_node tetra-functional nodes connected by $n_p_i polymer chains with $mpc_i monomers each"
puts " in a cubic simulation box of length [setmd box_l] at a density $density which corresponds to a network packing fraction $pack_i."
# if { ![file exists "$name_i$ident.wrm" ] && ![file exists "$name_i$ident.crl" ] && ![file exists "$name_i$ident.end" ] } {
inter 0 HARMONIC $fene_k $fene_r
# inter 0 FENE $fene_k $fene_r
for {set ia1 0} {$ia1<3} {incr ia1} {
for {set ia2 0} {$ia2<3} {incr ia2} {
inter $ia1 $ia2 lennard-jones $lj1_eps $lj1_sig $lj1_cut $lj1_shift 0
}
}
puts "Interaction Bonds: [inter 0]"
puts -nonewline "Creating diamond polymers of (initial) bond-length $bond_l... "; flush stdout
puts "Done ([diamond $a_cube $bond_l $mpc_i counterions $N_CI charges 1. 1. -1.])."
if { $vmd_output=="yes" } {
puts -nonewline "Write psf and pdb for VMD connection... "; flush stdout
prepare_vmd_connection "$name_i$ident"; puts "Done."
}
# }
#############################################################
# Warm-up Integration (with capped LJ-potential) #
#############################################################
puts -nonewline "\nStart warm-up integration (capped LJ-interactions) for maximal [expr $warm_step*$warm_loop] timesteps in $warm_loop loops; "
puts "stop if minimal distance is larger than $min_dist after at least [expr $warm_step*$min_loop] timesteps."
setmd time 0;
set tmp_cap $warm_cap1;
inter ljforcecap $tmp_cap;
inter coulomb 0.0
set obs_file [open "$name_i$ident.obs1" "w"]
puts $obs_file "t mindist re rg rh Temp"
puts $obs_file "[setmd time] [analyze mindist] [analyze re 8 $n_p_i $mpc_i] [analyze rg] [analyze rh] [setmd temp]"
puts -nonewline " Analysis at t=[setmd time]: mindist=[analyze mindist], "
puts "re=[lindex [analyze re] 0], rg=[lindex [analyze rg] 0], rh=[lindex [analyze rh] 0], T=[setmd temp]."
for { set j 0 } { $j < $warm_loop } { incr j } {
integrate $warm_step;
set tmp_dist [analyze mindist]
if { $vmd_output=="yes" } { imd positions }
puts -nonewline " \[$i\] Step [expr ($j+1)*$warm_step]/[expr $warm_step*$warm_loop] (t=[setmd time]): "; flush stdout
set tmp_Temp [expr [analyze energy kin]/$n_part/1.5]; puts -nonewline "LJ's cap = $tmp_cap, Temp = $tmp_Temp"; flush stdout
puts $obs_file "[setmd time] [analyze mindist] [analyze re] [analyze rg] [analyze rh] $tmp_Temp"
puts -nonewline ", mindist=[analyze mindist], re=[lindex [analyze re] 0], rg=[lindex [analyze rg] 0], rh=[lindex [analyze rh] 0]...\r"
flush stdout
if { ($tmp_dist >= $min_dist) && ($j > $min_loop) } { break }
inter forcecap $tmp_cap; set tmp_cap [expr $tmp_cap + $warm_incr]
}
flush $obs_file; close $obs_file
#############################################################
# Integration #
#############################################################
setmd time 0; set int_loop [expr int($int_time_i/([setmd time_step]*$int_step_i)+0.56)]; set tmp_step 0
puts "\nStart integration (full interactions) with timestep [setmd time_step] until time t>=$int_time_i (-> $int_loop loops). "
puts -nonewline " Activating electrostatics... "; flush stdout
puts "Done.\n[inter coulomb $bjerrum p3m tune accuracy $accuracy]"
puts -nonewline "Remove capping of LJ-interactions... "; flush stdout; inter forcecap 0; puts "Done."
set sfx "[expr int(ceil(log10($int_loop*$int_step_i)))+1]d"
set tmp_start 0; set obs_file [open "$name_i$ident.obs2" "w"]
set ptot [eval concat [eval concat [analyze pressure]]]; set p1 [lindex $ptot 0]
puts $obs_file "t mindist re dre re2 dre2 rg drg rg2 drg2 rh drh Temp p p2 ideal pid FENE pf pf2 lj plj plj2 coulomb pc pc2"
puts $obs_file "[setmd time] [analyze mindist] [analyze re 8 $n_p_i $mpc_i] [analyze rg] [analyze rh] [setmd temp] $ptot"
puts -nonewline " Analysis at t=[setmd time]: mindist=[analyze mindist], "
puts "re=[lindex [analyze re] 0], rg=[lindex [analyze rg] 0], rh=[lindex [analyze rh] 0], T=[setmd temp], p=$p1."
analyze append
#checkpoint_set "$name_i$ident.[eval format %0$sfx 0]" "all" "tmp_step"
for { set j $tmp_start } { $j < $int_loop } { incr j } {
integrate $int_step_i; set tmp_dist [analyze mindist]
if { $vmd_output=="yes" } { imd positions }
set tmp_step [expr ($j+1)*$int_step_i]
puts -nonewline " \[$i\] Step $tmp_step/[expr $int_step_i*$int_loop] (t=[setmd time]): "; flush stdout
set tmp_Temp [expr [analyze energy kin]/$n_part/1.5]; puts -nonewline "Temp = $tmp_Temp"; flush stdout
set ptot [eval concat [eval concat [analyze pressure]]]; set p1 [lindex $ptot 0]
puts $obs_file "[setmd time] [analyze mindist] [analyze re] [analyze rg] [analyze rh] $tmp_Temp $ptot"
set tmp_conf [analyze append]; flush $obs_file
puts -nonewline ", mindist=[analyze mindist], re=[lindex [analyze re] 0], "
puts -nonewline "rg=[lindex [analyze rg] 0], rh=[lindex [analyze rh] 0], p=$p1...\r"; flush stdout
}
puts -nonewline "\n Integration complete; saving checkpoint to '$name_i$ident.end'... ";flush stdout
polyBlockWriteAll "$name_i$ident.end" "-" "-"; puts "Done."; close $obs_file
puts -nonewline "\nFinished with current system; "
puts -nonewline "Cleaning up for next system... "; flush stdout;
# part deleteall;
analyze remove;
setmd time 0;
inter coulomb 0.0;
incr i;
puts "Done.\n"
}
}
# Wrapping up
puts -nonewline "Closing files... "; flush stdout
close $DHN_file
puts -nonewline "Compressing outputs to save disk-space... "; flush stdout
eval exec gzip *.obs2 *.ps *00
puts "Done."
puts "\nThe Diamond Hydrogel Networks Testcase is now complete.\nThanks for watching, and Good Night!\n"
exit
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ESPResSo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
set lock ".lock-[pid]"
proc checklock {} {
global lock
if {! [file exists $lock]} {quit} {after 200 checklock}
}
menu main off
axes location off
mol load vtf case1.vtf
rock off
mol modstyle 0 0 CPK 1.500000 0.600000 8.000000 6.000000
mol modcolor 0 0 Name
exec touch $lock
while { [catch {imd connect localhost 10000}] } { after 500 }
checklock
{variable
{box_l 64.7214 64.7214 64.7214}
{cell_grid 2 2 2}
{cell_size 32.3607 32.3607 32.3607}
{gamma 1.0}
{local_box_l 64.7214 64.7214 64.7214}
{max_num_cells 512}
{periodicity 0 0 0}
{skin 1.0}
{time 0.0}
{time_step 0.01}
{timings 0}
{transfer_rate 0}
}
{interactions
{0 FENE 7.0 2.0}
{0 0 lennard-jones 1.0 1.0 1.12246 1.0 0.0 0.0 }
{0 1 lennard-jones 1.0 1.0 1.12246 1.0 0.0 0.0 }
{1 1 lennard-jones 1.0 1.0 1.12246 1.0 0.0 0.0 }
{coulomb 0.0 dh 0 0}
}
{particles {id pos type q v f}
{0 16.1803 19.5137 32.3607 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{1 17.259 20.1803 31.9487 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{2 18.3377 20.847 31.5366 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{3 19.4164 21.5137 31.1246 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{4 20.4951 22.1803 30.7126 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{5 16.1803 18.1803 32.3607 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{6 16.1803 16.847 32.3607 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{7 16.1803 15.5137 32.3607 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{8 16.1803 14.1803 32.3607 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{9 21.5738 22.847 30.3006 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{10 21.1618 23.9257 29.6339 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{11 20.7497 25.0044 28.9672 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{12 20.3377 26.0831 28.3006 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{13 19.9257 27.1618 27.6339 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{14 22.6525 22.1803 29.8885 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{15 23.7312 21.5137 29.4765 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{16 24.8099 20.847 29.0645 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{17 25.8885 20.1803 28.6525 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{18 19.5137 28.2405 26.9672 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{19 18.1803 28.2405 26.9672 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{20 16.847 28.2405 26.9672 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{21 15.5137 28.2405 26.9672 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{22 14.1803 28.2405 26.9672 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{23 20.1803 28.6525 25.8885 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{24 20.847 29.0645 24.8099 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{25 21.5137 29.4765 23.7312 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{26 22.1803 29.8885 22.6525 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{27 12.847 28.2405 26.9672 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{28 12.435 27.1618 27.6339 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{29 12.023 26.0831 28.3006 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{30 11.6109 25.0044 28.9672 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{31 11.1989 23.9257 29.6339 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{32 12.1803 28.6525 25.8885 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{33 11.5137 29.0645 24.8099 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{34 10.847 29.4765 23.7312 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{35 10.1803 29.8885 22.6525 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{36 10.7869 22.847 30.3006 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{37 11.8656 22.1803 30.7126 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{38 12.9443 21.5137 31.1246 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{39 14.023 20.847 31.5366 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{40 15.1017 20.1803 31.9487 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{41 9.7082 22.1803 29.8885 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{42 8.62951 21.5137 29.4765 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{43 7.55083 20.847 29.0645 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{44 6.47214 20.1803 28.6525 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{45 16.1803 19.5137 0.0 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{46 17.259 20.1803 0.412023 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{47 18.3377 20.847 0.824045 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{48 19.4164 21.5137 1.23607 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{49 20.4951 22.1803 1.64809 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{50 16.1803 18.1803 0.0 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{51 16.1803 16.847 0.0 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{52 16.1803 15.5137 0.0 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{53 16.1803 14.1803 0.0 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{54 21.5738 22.847 2.06011 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{55 21.1618 23.9257 2.72678 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{56 20.7497 25.0044 3.39345 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{57 20.3377 26.0831 4.06011 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{58 19.9257 27.1618 4.72678 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{59 22.6525 22.1803 2.47214 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{60 23.7312 21.5137 2.88416 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{61 24.8099 20.847 3.29618 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{62 25.8885 20.1803 3.7082 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{63 19.5137 28.2405 5.39345 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{64 18.1803 28.2405 5.39345 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{65 16.847 28.2405 5.39345 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{66 15.5137 28.2405 5.39345 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{67 14.1803 28.2405 5.39345 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{68 20.1803 28.6525 6.47214 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{69 20.847 29.0645 7.55083 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{70 21.5137 29.4765 8.62951 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{71 22.1803 29.8885 9.7082 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{72 12.847 28.2405 5.39345 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{73 12.435 27.1618 4.72678 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{74 12.023 26.0831 4.06011 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{75 11.6109 25.0044 3.39345 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{76 11.1989 23.9257 2.72678 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{77 12.1803 28.6525 6.47214 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{78 11.5137 29.0645 7.55083 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{79 10.847 29.4765 8.62951 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{80 10.1803 29.8885 9.7082 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{81 10.7869 22.847 2.06011 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{82 11.8656 22.1803 1.64809 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{83 12.9443 21.5137 1.23607 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{84 14.023 20.847 0.824045 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{85 15.1017 20.1803 0.412023 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{86 9.7082 22.1803 2.47214 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{87 8.62951 21.5137 2.88416 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{88 7.55083 20.847 3.29618 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{89 6.47214 20.1803 3.7082 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{90 16.1803 12.847 32.3607 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{91 17.259 12.1803 31.9487 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{92 18.3377 11.5137 31.5366 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{93 19.4164 10.847 31.1246 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{94 20.4951 10.1803 30.7126 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{95 21.5738 9.51367 30.3006 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{96 21.1618 8.43498 29.6339 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{97 20.7497 7.35629 28.9672 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{98 20.3377 6.27761 28.3006 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{99 19.9257 5.19892 27.6339 0 1.0 0.0 0.0 0.0 0.0 0.0 0.0}
{100 22.6525 10.1803 29.8885 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
{101 23.7312 10.847 29.4765 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0}
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