X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fjobfiles.py;h=be88312d735de04d824c0d22338c920fb6d22c38;hb=ae2ca9f762ec4db6c91066465f347fc3678cddae;hp=048e03092ec353681e72250e936db49185bb11e0;hpb=2dc2941290afa8acdf82d37f1828110e2d257b61;p=django_unres.git diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py index 048e030..be88312 100644 --- a/django_simple/todo/jobfiles.py +++ b/django_simple/todo/jobfiles.py @@ -14,16 +14,18 @@ logging.basicConfig() logger = logging.getLogger(__name__) def write_ssbond(ssbond): - list=[] + list=[] + if ssbond!='': + ssbond=json.loads(ssbond) for e in ssbond: list.append(e[0]) list.append(e[1]) list_sorted=sorted(list) - if len(list)>0: + if len(list)>0: return str(len(list))+' '+' '.join(map(str,list_sorted))+'\n'+\ str(len(ssbond))+' '+' '.join(map(str,list))+'\n' - else: + else: return '0\n' @@ -41,12 +43,21 @@ def write_on_task_save(sender, instance, **kwargs): #wrapper = textwrap.TextWrapper(width=70) #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep))) - w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 & + if instance.unres_ff =='E0LL2Y': + w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 & WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 & WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 & WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25 & CUTOFF=7.00000 WCORR4=0.00000 """ + else: + w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542 & +WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000 & +WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000 & +WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000 & +CUTOFF=7.00000 WCORR4=0.00000 +""" + with open(instance.jobdirname+'/file.inp','w') as f: f.write(instance.name + ' UNRES server job'+ '\n') @@ -117,7 +128,7 @@ CUTOFF=7.00000 WCORR4=0.00000 type_line = 'reset_vel='+ str(instance.remd_nstex)\ +' nstep='+str(instance.md_nstep)\ +' ntwe='+str(instance.md_ntwe)\ - +' ntwx='+str(instance.remd_nstex)\ + +' ntwx='+str(instance.md_ntwx)\ +' dt='+str(instance.md_dt) if instance.md_lang == 'langevin': type_line = type_line + ' lang=1 ' @@ -133,7 +144,7 @@ CUTOFF=7.00000 WCORR4=0.00000 type_line2 = 'nrep='+str(instance.remd_nrep) \ +' nstex='+str(instance.remd_nstex) \ +' tlist mlist sync nsyn='+str(instance.remd_nstex)\ - +' traj1file rest1file ' + +' traj1file rest1file TRAJCACHE=200' if instance.md_start == 'pdbstart': type_line = type_line + ' preminim cart' @@ -206,12 +217,18 @@ CUTOFF=7.00000 WCORR4=0.00000 if instance.type == 'min': os.chdir(instance.jobdirname) - shutil.copy('../files/pbs.csh','.') + if instance.unres_ff =='E0LL2Y': + shutil.copy('../files/pbs.csh','.') + else: + shutil.copy('../files/pbs_new.csh','pbs.csh') ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) os.chdir('..') elif instance.type == 'md': os.chdir(instance.jobdirname) - f1 = open('../files/pbs_md.csh', 'r') + if instance.unres_ff =='E0LL2Y': + f1 = open('../files/pbs_md.csh', 'r') + else: + f1 = open('../files/pbs_md_new.csh', 'r') f2 = open('pbs.csh', 'w') for line in f1: f2.write(line.replace('$dimen3',str(dimen3) )) @@ -226,9 +243,9 @@ CUTOFF=7.00000 WCORR4=0.00000 ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) os.chdir('..') else: +# instance.type == 'remd' tmp1=json.loads(instance.remd_multi_m) nreplicas=sum(map(int, tmp1)) - # hardcoded for 4 core nodes with FGPROC=2 nodes=int(nreplicas*2/4) reszta = nreplicas*2-nodes*4 @@ -236,26 +253,43 @@ CUTOFF=7.00000 WCORR4=0.00000 pbs = '#PBS -l nodes='+str(nodes)+':ppn=4' else: pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta) + + tmp_ss='' + ix=0 + if seq[0]=='X': + ix=1 + if instance.ssbond!='': + l=[] + ss=json.loads(instance.ssbond) + for e in ss: + l.append(e[0]-ix) + l.append(e[1]-ix) + tmp_ss=' '.join(map(str,l)) os.chdir(instance.jobdirname) - f1 = open('../files/pbs8.csh', 'r') + if instance.unres_ff =='E0LL2Y': + f1 = open('../files/pbs8.csh', 'r') + else: + f1 = open('../files/pbs8_new.csh', 'r') f2 = open('pbs8.csh', 'w') for line in f1: if '#PBS -l nodes=4:ppn=4' in line: f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs)) + elif '$ssbond' in line: + f2.write(line.replace('$ssbond',tmp_ss)) else: tmp1=json.loads(instance.remd_multi_t) - f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'"')) + f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas))) f1.close() f2.close() os.chdir('..') # write wham & cluster input with open(instance.jobdirname+'/file_wham.inp','w') as f: - if instance.md_nstep/instance.remd_nstex*nreplicas<=8000: + if instance.md_nstep/instance.md_ntwx*nreplicas<=8000: isampl=1 else: - isampl=int(instance.md_nstep/instance.remd_nstex*nreplicas/8000) + isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000) if instance.md_pdbref: f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+ @@ -277,7 +311,7 @@ CUTOFF=7.00000 WCORR4=0.00000 for element in tmp1: f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n') f.write('kh= 0.0 Q0=0.0\n') - rec=instance.md_nstep/instance.remd_nstex + rec=instance.md_nstep/instance.md_ntwx f.write('nfile_cx=1 rec_start='+str(rec/10) +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n') f.write('file_MD000\n')