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dPaCSparallelGROMACS.py
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from __future__ import print_function
import sys, math, numpy, os, re
from subprocess import call
from multiprocessing import Pool
#################################################
# PaCS MD for GROMACS
# Number of data should to be the same with
# number of frames
# DATE updated: Apr 7th 2015
# Apr. 8 2015: change for loop for m to for m in range(1,nbin+1)
# Apr. 24 2015: adding if there is itp file, copy that file to working directory
# May 18 2015: adding restart to code
# June 16 2015: adding cutoff stop for distance in z direction
# Jan 24 2021: adding support for parallel multidir option in GROMACS:
# to run in serial mode, set runmode to 1
# to run in parallel mode, set the runmode to number of parallel process
# Oct 27 2021: fixing the mixing multiprocessing of python and denial executibility of MPI process on Fugaku
# Dec 02 2021: rearrange the code
#################################################
nbin=30 #number of replicas of PaCS-MD to run
nround=100 #number of cycles of PaCS-MD to run
rest=0 #set this < 0 to begin the new PaCSMD simulation, == 0 for automatic restart
restep=2 #this parameter only use when rest is set greater than 0, this give the specific step to run
nroundadd=100 #this parameter only use when rest is set greater than 0, this is the number of cycle to add to
comdistmax=7.0 #stop PaCS-MD when reaching this value
######################CV setting#############################
groupA="Protein"
groupB="DNA"
#####################input files setting#####################
grofn="input.gro"
mdfn="mdpacs.mdp"
mdinitfn="md.mdp"
vfn=""
ndxfn="index.ndx"
topolfn="topol.top"
itpfn="*.itp"
comdistfn="comdist"
outfnpf="pacs"
logfn="pacs.log"
selfn="seltext.txt"
skipdata=2
#######################clean trajectory option###############
clntrj=True
keepgroup="non-Water"
clnimdtraj=True
##################GROMACS run-setting########################
runmode=30 #using for multidir option in GROMACS
runmode2=4 #using for multiprocessing package of python within a node.
gmxcommand=" gmx_mpi "
mpicommand="mpirun -np "
usemp=True #use Multiprocessing library from Python
if usemp==True:
gmxcmd="gmx_serial " #change it to exact non-MPI version of GROMACS
else:
gmxcmd=mpicommand+" 1 "+gmxcommand #gmx serial calling
gmxcmd2=mpicommand+str(runmode)+" "+gmxcommand #call MPI task in this variable
gpu=-1 #use negative number for system choice of MD running conf.
gpuid="0011"
ntomp=50
wdir=os.getcwd()
outfn=wdir+"/"+outfnpf
#################################################
# Subroutine is below:
#################################################
def gmxcmd2lastloop(runmodelastloop):
tmpstr=mpicommand+str(runmodelastloop)+" gmx_mpi "
return tmpstr
def GROcheck():
os.system(gmxcmd+" --version | grep 'GROMACS version' > gmxversion ")
f=open("gmxversion","r")
ln=f.readlines()
vers=ln[0].split()[-1].split(".")[0]
return vers
def writesel(fn,txt):
f=open(fn,"w")
f.write(txt)
f.close()
return fn
def checkcycle():
n=1
chkfile=True
while chkfile:
print("Currently check cycle "+str(n)+"!")
failcyc=0
for cnt in range(1,nbin+1):
if not(os.path.exists(outfn+"-"+str(n)+"-"+str(cnt)+"/topol.tpr")):
chkfile=False
failcyc=cnt
break
if not(os.path.exists(outfn+"-"+str(n)+"-"+str(cnt)+"/confout.gro")):
chkfile=False
failcyc=cnt
break
if not(os.path.exists(outfn+"-"+str(n)+"-"+str(cnt)+"/traj_comp.xtc")):
chkfile=False
failcyc=cnt
break
if not(os.path.exists(outfn+"-"+str(n)+"-"+str(cnt)+"/"+outfnpf+"-"+str(n)+"-"+str(cnt)+".xvg")):
chkfile=False
failcyc=cnt
break
if not(os.path.exists(outfn+"-"+str(n)+"-"+str(cnt)+"/input.gro")):
chkfile=False
failcyc=cnt
break
if not(os.path.exists(outfn+"-"+str(n)+"-"+str(cnt)+"/ener.edr")):
chkfile=False
failcyc=cnt
break
if not(os.path.exists(outfn+"-"+str(n)+"-"+str(cnt)+"/md.log")):
chkfile=False
failcyc=cnt
break
n=n+1
print("Simulation was terminated at CYCLE "+str(n-1)+" and REPLICA "+str(cnt)+". Simulation will restart at this cycle.")
return n-1
def fn(m):
global n,comdistcp
#create directory
os.system("mkdir "+outfn+"-"+str(n)+"-"+str(m))
#dump frame to folder for MD run
if usemp==True:
os.system("echo 'System' | "+gmxcmd+" trjconv -f "+outfn+"-"+str(n-1)+"-"+str(int(comdistcp[len(comdistcp[:,0])-m,2]))+"/traj_comp.xtc -s "+outfn+"-"+str(n-1)+"-"+str(int(comdistcp[len(comdistcp[:,0])-m,2]))+"/topol.tpr -o "+outfn+"-"+str(n)+"-"+str(m)+"/input.gro -dump "+str(float(comdistcp[len(comdistcp[:,0])-m,0])) )
else:
os.system(mpicommand+" 1 --stdin "+wdir+"/"+selfn+".system"+ gmxcommand+" trjconv -f "+outfn+"-"+str(n-1)+"-"+str(int(comdistcp[len(comdistcp[:,0])-m,2]))+"/traj_comp.xtc -s "+outfn+"-"+str(n-1)+"-"+str(int(comdistcp[len(comdistcp[:,0])-m,2]))+"/topol.tpr -o "+outfn+"-"+str(n)+"-"+str(m)+"/input.gro -dump "+str(float(comdistcp[len(comdistcp[:,0])-m,0])) )
#copy needed file for MD run
os.system("cp -r "+wdir+"/"+mdfn+" "+outfn+"-"+str(n)+"-"+str(m)+"/")
os.system("cp -r "+wdir+"/"+topolfn+" "+outfn+"-"+str(n)+"-"+str(m)+"/")
if len(itpfn)>0:
os.system("cp -r "+wdir+"/"+itpfn+" "+outfn+"-"+str(n)+"-"+str(m)+"/")
os.system("cp -r "+wdir+"/index.ndx"+" "+outfn+"-"+str(n)+"-"+str(m)+"/")
#running simulation with random vel (set in mdp file)
if vers <=2016:
os.system(gmxcmd+" grompp -f "+outfn+"-"+str(n)+"-"+str(m)+"/"+mdfn+" -c "+outfn+"-"+str(n)+"-"+str(m)+"/input.gro -n "+ndxfn+" -o "+outfn+"-"+str(n)+"-"+str(m)+"/topol.tpr -maxwarn 10")
else:
os.system(gmxcmd+" grompp -f "+outfn+"-"+str(n)+"-"+str(m)+"/"+mdfn+" -c "+outfn+"-"+str(n)+"-"+str(m)+"/input.gro -n "+ndxfn+" -o "+outfn+"-"+str(n)+"-"+str(m)+"/topol.tpr -r "+grofn+" -maxwarn 10")
return
def f2(m):
global n
if usemp==True:
#apply nopbc for calculating the CV
os.system("echo 'non-Water' | "+gmxcmd+" trjconv -s "+outfn+"-"+str(n)+"-"+str(m)+"/topol.tpr -f "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp.xtc -o "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-nowat.xtc -pbc mol -ur compact")
os.system("mv "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-nowat.xtc "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp.xtc ")
#remove the noPBC trajectories
os.system("rm -r "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-noPBC.xtc")
else:
#apply nopbc for calculating the CV
os.system(mpicommand+" 1 --stdin "+wdir+"/"+selfn+".keepgroup "+ gmxcommand+" trjconv -s "+outfn+"-"+str(n)+"-"+str(m)+"/topol.tpr -f "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp.xtc -o "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-nowat.xtc -pbc mol -ur compact")
os.system("mv "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-nowat.xtc "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp.xtc ")
#remove the noPBC trajectories
os.system("rm -r "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-noPBC.xtc")
return
def f1a(m):
global n
#apply nopbc for calculating the CV
if usemp==True:
os.system("echo 'non-Water' | "+gmxcmd+" trjconv -s "+outfn+"-"+str(n)+"-"+str(m)+"/topol.tpr -f "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp.xtc -o "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-nowat.xtc -pbc mol -ur compact")
os.system("mv "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-nowat.xtc "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp.xtc ")
else:
os.system(mpicommand+" 1 --stdin "+wdir+"/"+selfn+".keepgroup "+ gmxcommand+" trjconv -s "+outfn+"-"+str(n)+"-"+str(m)+"/topol.tpr -f "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp.xtc -o "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-nowat.xtc -pbc mol -ur compact")
os.system("mv "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-nowat.xtc "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp.xtc ")
return
def f1b(m):
global n
#remove the noPBC trajectories
os.system("rm -r "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-noPBC.xtc")
return
def f(m):
global n
#apply nopbc for calculating the CV
if usemp==True:
os.system("echo 'System' | "+gmxcmd+" trjconv -s "+outfn+"-"+str(n)+"-"+str(m)+"/topol.tpr -f "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp.xtc -o "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-noPBC.xtc -pbc mol -ur compact")
#calculating the CV of the run
os.system(gmxcmd+" distance -f "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-noPBC.xtc -s "+outfn+"-"+str(n)+"-"+str(m)+"/topol.tpr -n "+ndxfn+" -oall "+outfn+"-"+str(n)+"-"+str(m)+"/"+outfnpf+"-"+str(n)+"-"+str(m)+".xvg -xvg none -tu ps -sf "+wdir+"/sel.dat")
else:
os.system(mpicommand+" 1 --stdin "+wdir+"/"+selfn+".system "+ gmxcommand+" trjconv -s "+outfn+"-"+str(n)+"-"+str(m)+"/topol.tpr -f "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp.xtc -o "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-noPBC.xtc -pbc mol -ur compact")
#calculating the CV of the run
os.system(gmxcmd+" distance -f "+outfn+"-"+str(n)+"-"+str(m)+"/traj_comp-noPBC.xtc -s "+outfn+"-"+str(n)+"-"+str(m)+"/topol.tpr -n "+ndxfn+" -oall "+outfn+"-"+str(n)+"-"+str(m)+"/"+outfnpf+"-"+str(n)+"-"+str(m)+".xvg -xvg none -tu ps -sf "+wdir+"/sel.dat")
return
#################################################
# Main program is below:
#################################################
#check version of GROMACS
#vers=GROcheck()
vers=2021.3
#vers=re.sub("[^\d\.]", "", GROcheck())
######write selection file#####
writesel(wdir+"/sel.dat",'com of group "'+groupA+'" plus com of group "'+groupB+'"\n')
#system
writesel(wdir+"/"+selfn+".system",'System\n')
#keepgroup
writesel(wdir+"/"+selfn+".keepgroup",keepgroup+"\n")
if rest<0:
#save the old log file
if os.path.exists(wdir+"/"+logfn):
i=0
while(os.path.exists(wdir+"/"+logfn+"."+str(i))):
i=i+1
os.system("mv "+wdir+"/"+logfn+" "+wdir+"/"+logfn+"."+str(i))
os.system("echo 'PaCS MD is going to run ' > "+wdir+"/"+logfn)
print("PaCS MD is going to run \n")
os.system("echo 'Number of BIN is "+str(nbin)+" ' >> "+wdir+"/"+logfn)
print("echo 'Number of BIN is "+str(nbin)+"\n")
os.system("echo 'Number of ROUND is "+str(nround)+" ' >> "+wdir+"/"+logfn)
print("echo 'Number of ROUND is "+str(nround)+"\n")
os.system("echo 'Simulation is running from the beginning. ' >> "+wdir+"/"+logfn)
print("Simulation is running from the beginning. \n")
#call gromacs to run for the first cycle
os.system("echo '++++++++++++++++' >> "+wdir+"/"+logfn)
print('++++++++++++++++\n')
os.system("echo 'ROUND 0. ' >> "+wdir+"/"+logfn)
print('ROUND 0. \n')
os.system("echo '1111 Max to Min Ranking 1111' >> "+wdir+"/"+logfn)
print('+ Ranking +\n' )
os.system("echo '+ Bin +++ Step +' >> "+wdir+"/"+logfn)
print('+ Bin +++ Step +\n')
os.system("mkdir "+outfn+"-0-0")
#copy needed file for MD run
os.system("cp -r "+wdir+"/"+mdinitfn+" "+outfn+"-0-0/")
os.system("cp -r "+wdir+"/"+topolfn+" "+outfn+"-0-0/")
if len(itpfn)>0:
os.system("cp -r "+wdir+"/"+itpfn+" "+outfn+"-0-0/")
os.system("cp -r "+wdir+"/"+grofn+" "+outfn+"-0-0/")
if len(vfn)>0:
os.system("cp -r "+wdir+"/"+vfn+" "+outfn+"-0-0/")
if vers<=2016:
os.system(gmxcmd+" grompp -f "+outfn+"-0-0/"+mdinitfn+" -c "+outfn+"-0-0/"+grofn+" -t "+outfn+"-0-0/"+vfn+" -p "+outfn+"-0-0/"+topolfn+" -n "+ndxfn+" -o "+outfn+"-0-0/topol.tpr -maxwarn 10")
else:
os.system(gmxcmd+" grompp -f "+outfn+"-0-0/"+mdinitfn+" -c "+outfn+"-0-0/"+grofn+" -t "+outfn+"-0-0/"+vfn+" -p "+outfn+"-0-0/"+topolfn+" -n "+ndxfn+" -o "+outfn+"-0-0/topol.tpr -r "+grofn+" -maxwarn 10")
else:
if vers<=2016:
os.system(gmxcmd+" grompp -f "+outfn+"-0-0/"+mdinitfn+" -c "+outfn+"-0-0/"+grofn+" -p "+outfn+"-0-0/"+topolfn+" -n "+ndxfn+" -o "+outfn+"-0-0/topol.tpr -maxwarn 10")
else:
os.system(gmxcmd+" grompp -f "+outfn+"-0-0/"+mdinitfn+" -c "+outfn+"-0-0/"+grofn+" -p "+outfn+"-0-0/"+topolfn+" -n "+ndxfn+" -o "+outfn+"-0-0/topol.tpr -r "+grofn+" -maxwarn 10")
print("################################")
if gpu>=0 and ntomp>0:
os.system(gmxcmd2+" mdrun -s "+outfn+"-0-0/topol.tpr -o "+outfn+"-0-0/traj.trr -x "+outfn+"-0-0/traj_comp.xtc -e "+outfn+"-0-0/ener.edr -g "+outfn+"-0-0/md.log -c "+outfn+"-0-0/confout.gro -cpo "+outfn+"-0-0/state.cpt -pme gpu -npme 1 -v -ntomp "+str(ntomp)+" -gpu_id "+str(gpuid))
else:
os.system(gmxcmd2+" mdrun -s "+outfn+"-0-0/topol.tpr -o "+outfn+"-0-0/traj.trr -x "+outfn+"-0-0/traj_comp.xtc -e "+outfn+"-0-0/ener.edr -g "+outfn+"-0-0/md.log -c "+outfn+"-0-0/confout.gro -cpo "+outfn+"-0-0/state.cpt -pme gpu -npme 1 -v -ntomp "+str(ntomp))
#apply nopbc for calculating the rmsd
os.system(mpicommand+" 1 --stdin "+wdir+"/"+selfn+".system "+ gmxcommand+" trjconv -s "+outfn+"-0-0/topol.tpr -f "+outfn+"-0-0/traj_comp.xtc -o "+outfn+"-0-0/traj_comp-noPBC.xtc -pbc mol -ur compact")
print(mpicommand+" 1 --stdin "+wdir+"/"+selfn+".system "+ gmxcommand+" trjconv -s "+outfn+"-0-0/topol.tpr -f "+outfn+"-0-0/traj_comp.xtc -o "+outfn+"-0-0/traj_comp-noPBC.xtc -pbc mol -ur compact")
#calculating the rmsd of the first cycle and pick up the 10 best one
os.system(gmxcmd+" distance -f "+outfn+"-0-0/traj_comp-noPBC.xtc -s "+outfn+"-0-0/topol.tpr -n "+ndxfn+" -oall "+outfn+"-0-0/"+outfnpf+"-0-0.xvg -xvg none -tu ps -sf "+wdir+"/sel.dat")
print(gmxcmd+" distance -f "+outfn+"-0-0/traj_comp-noPBC.xtc -s "+outfn+"-0-0/topol.tpr -n "+ndxfn+" -oall "+outfn+"-0-0/"+outfnpf+"-0-0.xvg -xvg none -tu ps -sf "+wdir+"/sel.dat")
if clnimdtraj==True:
os.system("rm -r "+outfn+"-0-0/traj_comp-noPBC.xtc")
#reading the rmsd
comdist=numpy.loadtxt(outfn+"-0-0/"+outfnpf+"-0-0.xvg",skiprows=skipdata)
comdistcp=numpy.concatenate((comdist,numpy.zeros((len(comdist[:,1]),1))),1)
comdistcp=comdistcp[numpy.lexsort((comdistcp[:,0],comdistcp[:,1]))]
#writing the ranking to log file
for m in range(1,nbin+1):
os.system("echo '"+str(comdistcp[len(comdistcp[:,0])-m,2])+" "+str(comdistcp[len(comdistcp[:,0])-m,0])+" "+str(comdistcp[len(comdistcp[:,0])-m,1])+"' >> "+wdir+"/"+logfn)
print(str(comdistcp[len(comdistcp[:,0])-m,2])+" "+str(comdistcp[len(comdistcp[:,0])-m,0])+" "+str(comdistcp[len(comdistcp[:,0])-m,1])+"\n")
else:
print("Simulation is going restart at ROUND "+str(nround)+ "\n" )
#checking the need of restart file or quit the program
if not(os.path.exists(wdir+"/"+logfn)):
print(logfn+" file is not found! Please check the file.")
exit()
f=open(wdir+"/"+logfn,'r')
linesfn=f.readlines()
f.close()
for m in range(0,len(linesfn)-1):
linesfn[m]=linesfn[m].rstrip('\n')
bn=int(linesfn[1][17:(len(linesfn[1]))])
print("BIN of current PACS MD is ",bn)
if rest!=0:
rnd=int(linesfn[2][19:(len(linesfn[2]))])
print("ROUND of current PACS MD is ",rnd)
if restep>rnd-1:
print("Restart round is larger than the number of round that we have. Please recheck")
exit()
elif rest==0:
rnd=checkcycle()
restep=rnd-1
print("ROUND of current PACS MD is ",rnd)
#re-executing the MD code for regenerating the last cycle
n=restep
if runmode==1:
for m in range(1,nbin+1):
if gpu>=0 and ntomp>0:
os.system(gmxcmd2+" mdrun -deffnm "+outfn+"-"+str(n)+"-"+str(m)+"/topol -v -ntomp "+str(ntomp)+" -gpu_id "+str(gpuid))
else:
os.system(gmxcmd2+" mdrun -deffnm "+outfn+"-"+str(n)+"-"+str(m)+"/topol -v -ntomp "+str(ntomp))
elif runmode>1:
mdloop=nbin//runmode
print("Expect number of mdloop "+str(mdloop))
if (mdloop*runmode)<nbin:
lastloop=nbin%runmode
mdloop=mdloop
else:
lastloop=0
print("Expect number of lastloop "+str(lastloop))
for x in range(0,mdloop):
multidir=" "
for m in range(x*runmode+1,(x+1)*runmode+1):
multidir=multidir+outfn+"-"+str(n)+"-"+str(m)+" "
if gpu>=0 and ntomp>0:
os.system(gmxcmd2+" mdrun -multidir "+multidir+" -s topol -ntomp "+str(ntomp)+" -gpu_id "+str(gpuid))
print(gmxcmd2+" mdrun -multidir "+multidir+" -s topol -v -ntomp "+str(ntomp)+" -gpu_id "+str(gpuid))
else:
os.system(gmxcmd2+" mdrun -multidir "+multidir+" -s topol -ntomp "+str(ntomp))
print(gmxcmd2+" mdrun -multidir "+multidir+" -s topol -v -ntomp "+str(ntomp))
if lastloop>0:
multidir=" "
for m in range(mdloop*runmode+1,nbin+1):
multidir=multidir+outfn+"-"+str(n)+"-"+str(m)+" "
print(gmxcmd2lastloop(lastloop))
if gpu>=0 and ntomp>0:
os.system(gmxcmd2lastloop(lastloop)+" mdrun -multidir "+multidir+" -s topol -ntomp "+str(ntomp)+" -gpu_id "+str(gpuid))
else:
os.system(gmxcmd2lastloop(lastloop)+" mdrun -multidir "+multidir+" -s topol -ntomp "+str(ntomp))
# rewrite the PACS MD log:
if os.path.exists(wdir+"/"+logfn):
i=0
while(os.path.exists(wdir+"/"+logfn+"."+str(i))):
i=i+1
os.system("mv "+wdir+"/"+logfn+" "+wdir+"/"+logfn+"."+str(i))
f=open(wdir+"/"+logfn,'w')
wrtstepneed=nbin*(restep+1)+4*(restep+1)+4
while wrtstepneed>len(linesfn):
rnd=rnd-1
restep=rnd
wrtstepneed=nbin*(restep+1)+4*(restep+1)+4
print("Due to the lack of data in "+wdir+"/"+logfn+". Resetting ROUND of current PACS MD is ",rnd)
for m in range(0,wrtstepneed):
if m==2:
f.write(linesfn[2][0:18]+" "+str(int(restep+nroundadd))+"\n")
elif (restep!=0) and (m==wrtstepneed-1-nbin-1):
f.write(linesfn[m]+"\n")
elif m==(wrtstepneed-1):
f.write(linesfn[m]+" ")
else:
f.write(linesfn[m]+"\n")
f.close()
#rebuild the comdist array
cdcptemp=[] #clean buffer array
for m in range(1,nbin+1):
if not(os.path.exists(outfn+"-"+str(restep)+"-"+str(m)+"/"+outfnpf+"-"+str(restep)+"-"+str(m)+".xvg")):
print("Distance file is not found! Please check the file!")
exit()
cdtemp=numpy.loadtxt(outfn+"-"+str(restep)+"-"+str(m)+"/"+outfnpf+"-"+str(restep)+"-"+str(m)+".xvg",skiprows=skipdata)
cdcptemp1=[]
cdcptemp1=numpy.concatenate((cdtemp,numpy.ones((len(cdtemp[:,1]),1))*(m)),1)
if m>1:
cdcptemp =numpy.concatenate((cdcptemp,cdcptemp1),0)
else:
cdcptemp=cdcptemp1
comdistcp=cdcptemp[numpy.lexsort((cdcptemp[:,0],cdcptemp[:,1]))]
#check for restart flag
if rest<0:
nbloop=1
else:
nbloop=restep+1
nround=restep+nroundadd+1
n=nbloop
while n<nround:
#for n in range(nbloop,nround):
cdcptemp=[] #clean buffer array
os.system("echo '++++++++++++++++' >> "+wdir+"/"+logfn)
print('++++++++++++++++\n')
os.system("echo 'ROUND "+str(n)+". ' >> "+wdir+"/"+logfn)
print("ROUND "+str(n)+"\n" )
os.system("echo '1111 Max to Min Ranking 1111' >> "+wdir+"/"+logfn)
print("++++ Ranking +++")
os.system("echo '+ Bin +++ Step +' >> "+wdir+"/"+logfn)
print("+ Bin +++ Step +")
#preparing the tpr files:
if usemp==True:
p=Pool(runmode2)
with p:
p.map(fn,[tmpvar for tmpvar in range(1,nbin+1)])
p.join()
p.close()
else:
for tmpvar in range(1,nbin+1):
fn(tmpvar)
#cleanning trajectories if being selected
if ((clntrj==True) and (clnimdtraj==True)):
if usemp==True:
p=Pool(runmode2)
with p:
p.map(f2,[tmpvar for tmpvar in range(1,nbin+1)] )
p.join()
p.close()
else:
for tmpvar in range(1,nbin+1):
f2(tmpvar)
elif ((clntrj==True) and (clnimdtraj==False)):
if usemp==True:
p=Pool(runmode2)
with p:
p.map(f1a,[tmpvar for tmpvar in range(1,nbin+1)] )
p.join()
p.close()
else:
for tmpvar in range(1,nbin+1):
f1a(tmpvar)
elif ((clntrj==False) and (clnimdtraj==True)):
if usemp==True:
p=Pool(runmode2)
with p:
p.map(f1b,[tmpvar for tmpvar in range(1,nbin+1)] )
p.join()
p.close()
else:
for tmpvar in range(1,nbin+1):
f1b(tmpvar)
#executing the MD code
if runmode==1:
for m in range(1,nbin+1):
if gpu>=0 and ntomp>0:
os.system(gmxcmd2+" mdrun -deffnm "+outfn+"-"+str(n)+"-"+str(m)+"/topol -v -ntomp "+str(ntomp)+" -gpu_id "+str(gpuid))
else:
os.system(gmxcmd2+" mdrun -deffnm "+outfn+"-"+str(n)+"-"+str(m)+"/topol -v -ntomp "+str(ntomp))
elif runmode>1:
mdloop=nbin//runmode
print("Expect number of mdloop "+str(mdloop))
if (mdloop*runmode)<nbin:
lastloop=nbin%runmode
mdloop=mdloop
else:
lastloop=0
print("Expect number of lastloop "+str(lastloop))
for x in range(0,mdloop):
multidir=" "
for m in range(x*runmode+1,(x+1)*runmode+1):
multidir=multidir+outfn+"-"+str(n)+"-"+str(m)+" "
if gpu>=0 and ntomp>0:
os.system(gmxcmd2+" mdrun -multidir "+multidir+" -s topol -ntomp "+str(ntomp)+" -gpu_id "+str(gpuid))
print(gmxcmd2+" mdrun -multidir "+multidir+" -s topol -v -ntomp "+str(ntomp)+" -gpu_id "+str(gpuid))
else:
os.system(gmxcmd2+" mdrun -multidir "+multidir+" -s topol -ntomp "+str(ntomp))
print(gmxcmd2+" mdrun -multidir "+multidir+" -s topol -v -ntomp "+str(ntomp))
if lastloop>0:
multidir=" "
for m in range(mdloop*runmode+1,nbin+1):
multidir=multidir+outfn+"-"+str(n)+"-"+str(m)+" "
print(gmxcmd2lastloop(lastloop))
if gpu>=0 and ntomp>0:
os.system(gmxcmd2lastloop(lastloop)+" mdrun -multidir "+multidir+" -s topol -ntomp "+str(ntomp)+" -gpu_id "+str(gpuid))
else:
os.system(gmxcmd2lastloop(lastloop)+" mdrun -multidir "+multidir+" -s topol -ntomp "+str(ntomp))
#check the distribution and add to temperary array
if usemp==True:
p=Pool(runmode2)
with p:
p.map(f,[tmpvar for tmpvar in range(1,nbin+1)] )
p.join()
p.close()
else:
for tmpvar in range(1,nbin+1):
f(tmpvar)
for m in range(1,nbin+1):
#reading the CV
cdtemp=numpy.loadtxt(outfn+"-"+str(n)+"-"+str(m)+"/"+outfnpf+"-"+str(n)+"-"+str(m)+".xvg",skiprows=skipdata)
cdcptemp1=[]
cdcptemp1=numpy.concatenate((cdtemp,numpy.ones((len(cdtemp[:,1]),1))*(m)),1)
if m>1:
cdcptemp =numpy.concatenate((cdcptemp,cdcptemp1),0)
else:
cdcptemp=cdcptemp1
#Preparing for the next PaCS MD step
#Ranking the trajectory
comdistcp=cdcptemp[numpy.lexsort((cdcptemp[:,0],cdcptemp[:,1]))]
#writing the ranking to log file
for l in range(1,nbin+1):
os.system("echo '"+str(comdistcp[len(comdistcp[:,0])-l,2])+" "+str(comdistcp[len(comdistcp[:,0])-l,0])+" "+str(comdistcp[len(comdistcp[:,0])-l,1])+"' >> "+wdir+"/"+logfn)
print(str(comdistcp[len(comdistcp[:,0])-l,2])+" "+str(comdistcp[len(comdistcp[:,0])-l,0])+" "+str(comdistcp[len(comdistcp[:,0])-l,1])+"\n")
if ((comdistmax>0.0) and (comdistcp[len(comdistcp[:,2])-nbin-1,1]<comdistmax) and (n==(nround-1))):
nround=nround+1
if ((comdistmax>0.0) and (comdistcp[len(comdistcp[:,2])-nbin-1,1]>comdistmax) and (n<(nround-1))):
break
n=n+1 #this command is for replacing "for" loop with "while" loop