forked from lijiext/lammps
add multi-replica example for gREM
This commit is contained in:
Axel Kohlmeyer
parent
fdf5d68f9f
commit
5f94b31806
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# LJ particles
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variable T0 equal 300.0
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variable press equal 0.0
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units real
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atom_style full
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pair_style lj/cut 5.0
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read_data "restart_file"
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thermo 10
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thermo_style custom step temp pe etotal press vol
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velocity all create ${T0} 12427
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timestep 1.0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxgREM all grem 400 -.01 -30000 fxnvt
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thermo_modify press fxgREM_press
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run 10000
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write_data final_restart_file
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,22 @@
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# LJ particles
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variable T0 equal 300.0
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variable press equal 0.0
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units real
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atom_style full
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pair_style lj/cut 5.0
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read_data "restart_file"
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thermo 10
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thermo_style custom step temp pe etotal press vol
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velocity all create ${T0} 12427
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timestep 1.0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxgREM all grem 405 -.01 -30000 fxnvt
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thermo_modify press fxgREM_press
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run 10000
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write_data final_restart_file
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,22 @@
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# LJ particles
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variable T0 equal 300.0
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variable press equal 0.0
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units real
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atom_style full
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pair_style lj/cut 5.0
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read_data "restart_file"
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thermo 10
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thermo_style custom step temp pe etotal press vol
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velocity all create ${T0} 12427
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timestep 1.0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxgREM all grem 410 -.01 -30000 fxnvt
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thermo_modify press fxgREM_press
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run 10000
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write_data final_restart_file
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,22 @@
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# LJ particles
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variable T0 equal 300.0
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variable press equal 0.0
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units real
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atom_style full
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pair_style lj/cut 5.0
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read_data "restart_file"
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thermo 10
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thermo_style custom step temp pe etotal press vol
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velocity all create ${T0} 12427
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timestep 1.0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxgREM all grem 415 -.01 -30000 fxnvt
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thermo_modify press fxgREM_press
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run 10000
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write_data final_restart_file
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,22 @@
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# LJ particles
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variable T0 equal 300.0
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variable press equal 0.0
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units real
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atom_style full
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pair_style lj/cut 5.0
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read_data "restart_file"
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thermo 10
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thermo_style custom step temp pe etotal press vol
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velocity all create ${T0} 12427
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timestep 1.0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxgREM all grem 420 -.01 -30000 fxnvt
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thermo_modify press fxgREM_press
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run 10000
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write_data final_restart_file
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,22 @@
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# LJ particles
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variable T0 equal 300.0
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variable press equal 0.0
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units real
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atom_style full
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pair_style lj/cut 5.0
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read_data "restart_file"
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thermo 10
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thermo_style custom step temp pe etotal press vol
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velocity all create ${T0} 12427
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timestep 1.0
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fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
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fix fxgREM all grem 425 -.01 -30000 fxnvt
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thermo_modify press fxgREM_press
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run 10000
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write_data final_restart_file
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,15 @@
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#/bin/bash
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for i in $(ls -d [0-9]*)
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do
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rm -f $i/final*
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rm -f $i/log*
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rm -f $i/ent*
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rm -f $i/output
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cp $i/restart.init $i/restart_file
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done
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echo 1 > lastexchange
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cp walker.bkp lastwalker
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exit 0
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#!/usr/bin/env python2.7
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import os, sys
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from numpy import *
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import numpy.random
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### Runs replica exchange with gREM (fix grem) for unlimited number of replicas on a set number of processors. This script is inefficient, but necessary if wanting to run with hundreds of replicas on relatively few number of procs.
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### read number of processors from the command line
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nproc = int(sys.argv[1])
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### path to simulation directory
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path = os.getcwd()
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### path to LAMMPS executable
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lmp = sys.argv[2]
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### LAMMPS input name
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inp = sys.argv[3]
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### define pressure for simulations (0 if const V)
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pressure = 0
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### some constants for gREM, must match with LAMMPS input file!
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H = -30000
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eta = -0.01
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#kB = 0.000086173324 # eV (metal)
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kB = 0.0019872 # kcal/mol (real)
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### define lambdas - script assumes that there are already existing directories with all files necessary to run
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lambdas=[400,405,410,415,420,425]
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ll = len(lambdas)
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### define number of exchanges
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starting_ex = int(loadtxt("lastexchange"))
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how_many_ex = 5
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max_exchange = starting_ex+how_many_ex
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### array with walkers
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walker = loadtxt("lastwalker")
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### initiate array with enthalpies
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enthalpy = zeros(ll)
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aver_enthalpy = zeros(ll)
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for exchange in arange(starting_ex,max_exchange):
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print "run", exchange
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for l in range(ll):
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#print "replica", l
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os.chdir(path+"/%s" % lambdas[l])
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#os.system("cp restart_file restart_file%d" % exchange)
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if (nproc > 1):
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os.system("mpirun -np %d " + lmp + " -in " + inp + " > output" % nproc)
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if (nproc == 1):
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os.system(lmp + " -in " + inp + " > output")
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os.system("grep -v '[a-zA-Z]' output | awk '{if(NF==6 && NR>19)print $0}' | awk '{print $3}' >ent")
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enthalpy[l] = os.popen("tail -n 1 ent").read()
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ee = loadtxt("ent")
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aver_enthalpy[l] = mean(ee[-1])
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# os.system("mv dump.dcd dump%d.dcd" % exchange)
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os.system("mv log.lammps log%d.lammps" % exchange)
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# os.system("rm output")
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os.system("mv final_restart_file final_restart_file%d" % exchange)
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os.system("mv ent ent%d" % exchange)
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os.system("bzip2 log%d.lammps ent%d" % (exchange,exchange))
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os.system("cp final_restart_file%d restart_file" % exchange)
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### replicas will be exchanged based on enthalpy order, not replicas order (termostat order)
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#entalpy_sorted_indices = enthalpy.argsort()
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aver_entalpy_sorted_indices = aver_enthalpy.argsort()
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### choose pair of replicas for exchange attempt based on enthalpy order
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pp = random.random_integers(0,ll-2)
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first = aver_entalpy_sorted_indices[pp]
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second = aver_entalpy_sorted_indices[pp+1]
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#if (first>second):
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# tmp = first
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# first = second
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# second = tmp
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print "pair1:", first, second
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### calculate weights for exchange criterion
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w1 = log(lambdas[first]+eta*(enthalpy[first]-1*H))
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w2 = log(lambdas[first]+eta*(enthalpy[second]-1*H))
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w3 = log(lambdas[second]+eta*(enthalpy[first]-1*H))
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w4 = log(lambdas[second]+eta*(enthalpy[second]-1*H))
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weight = (w4-w3+w1-w2)/eta/kB
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### generate randon number for exchange criterion and calc its log
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LOGRANDNUM = log(random.random())
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### wyzeruj warunki
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compare1 = 0
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compare2 = 0
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if (weight>0):
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compare1 = 1
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if (weight>LOGRANDNUM):
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compare2 = 1
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### exchange restart files if exchange condition is satisfied
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if (compare1>0 or compare2>0):
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print "exchange1 accepted for pair", first, second, lambdas[first], lambdas[second], "with compares as", compare1, compare2, "weight as", weight, "and lograndnum", LOGRANDNUM
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os.system("cp %s/%s/final_restart_file%d %s/%s/restart_file" % (path,lambdas[first],exchange,path,lambdas[second]))
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os.system("cp %s/%s/final_restart_file%d %s/%s/restart_file" % (path,lambdas[second],exchange,path,lambdas[first]))
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### update walkers
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tmp1=walker[first]
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tmp2=walker[second]
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walker[first]=tmp2
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walker[second]=tmp1
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else:
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print "exchange1 not accepted for pair", first, second, lambdas[first], lambdas[second], "with compares as", compare1, compare2, "weight as", weight, "and lograndnum", LOGRANDNUM
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### choose again pair of replicas for exchange attempt based on enthalpy order
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### but make sure this pair is different than the first pair
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if_different = 0
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while if_different<1:
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pp2 = random.random_integers(0,ll-2)
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third = aver_entalpy_sorted_indices[pp2]
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fourth = aver_entalpy_sorted_indices[pp2+1]
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if (third!=first and third!=second and third!=aver_entalpy_sorted_indices[pp-1]):
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if_different = 1
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print "pair2:", third, fourth
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### calculate weights for exchange criterion
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w1 = log(lambdas[third]+eta*(enthalpy[third]-1*H))
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w2 = log(lambdas[third]+eta*(enthalpy[fourth]-1*H))
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w3 = log(lambdas[fourth]+eta*(enthalpy[third]-1*H))
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w4 = log(lambdas[fourth]+eta*(enthalpy[fourth]-1*H))
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weight = (w4-w3+w1-w2)/eta/kB
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### generate randon number for exchange criterion and calc its log
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LOGRANDNUM = log(random.random())
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### wyzeruj warunki
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compare1 = 0
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compare2 = 0
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if (weight>0):
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compare1 = 1
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if (weight>LOGRANDNUM):
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compare2 = 1
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### exchange restart files if exchange condition is satisfied
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if (compare1>0 or compare2>0):
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print "exchange2 accepted for pair", third, fourth, lambdas[third], lambdas[fourth], "with compares as", compare1, compare2, "weight as", weight, "and lograndnum", LOGRANDNUM
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os.system("cp %s/%s/final_restart_file%d %s/%s/restart_file" % (path,lambdas[third],exchange,path,lambdas[fourth]))
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os.system("cp %s/%s/final_restart_file%d %s/%s/restart_file" % (path,lambdas[fourth],exchange,path,lambdas[third]))
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### update walkers
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tmp1=walker[third]
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tmp2=walker[fourth]
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walker[third]=tmp2
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walker[fourth]=tmp1
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else:
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print "exchange2 not accepted for pair", third, fourth, lambdas[third], lambdas[fourth], "with compares as", compare1, compare2, "weight as", weight, "and lograndnum", LOGRANDNUM
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#print "walkers:", walker
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print "".join(["%d " % x for x in walker])
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sys.stdout.flush()
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lastwalker = open(path + "/lastwalker", "w")
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lastwalker.write("".join(["%d " % w for w in walker]))
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lastwalker.close()
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lastexchange = open(path + "/lastexchange", "w")
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lastexchange.write("%d" % (exchange+1))
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lastexchange.close()
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#!/bin/sh
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NPROCS=1
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if [ $# -gt 0 ]; then
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NPROCS=$1
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fi
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bash ./clean.sh
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python ./double-re-short.py $NPROCS $HOME/compile/lammps-icms/src/lmp_omp in.gREM > total_output.$NPROCS
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exit 0
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@ -0,0 +1 @@
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0 1 2 3 4 5
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