added cmmde_orca feature

bin/cmmde.py

@@ -29,7 +29,7 @@ parser.add_argument('-sfreq','--scalefreq',type=float,default=1, help='Faktor sk
 # Input yang berkaitan dengan perhitungan menggunakan software DCDFTBMD
 parser.add_argument('-disp','--dispersion',type=str,default='None', help='Model koreksi dispersi jika menggunakan software DCDFTB. Pilihan: None, D3, D3BJ, D3H5.')
 parser.add_argument('-para','--parapath',type=str,default='/home/adit/opt/dftbplus-21.2/external/slakos/origin/3ob-3-1',help='Lokasi folder berisikan himpunan parameter DFTB yang akan digunakan.')
-parser.add_argument('-iter','--iter',type=int,default=500, help='Jumlah iterasi dalam optimasi geometri dan jenis perhitungan lainnya')
+parser.add_argument('-iter','--iter',type=int,default=9999, help='Jumlah iterasi dalam optimasi geometri dan jenis perhitungan lainnya')
 parser.add_argument('-ens','--ensembel',type=str,default='NVE', help='Ensembel yang digunakan dalam simulasi dinamika molekul. Pilihan: NVE, NVT, dan NPT.')
 parser.add_argument('-tstat','--thermostat',type=str,default='andersen', help='Termostat yang digunakan dalam simulasi NVT. Pilihan: andersen,berendsen,dan nose')
 parser.add_argument('-t','--temp', type=float, default=298.15,help='Suhu yang digunakan dalam perhitungan frekuensi maupun simulasi MD dalam satuan Kelvin.')
@@ -130,7 +130,7 @@ parser.add_argument('-scanmode','--scanmode',type=str,default='None',help='Mode
 parser.add_argument('-scan','--scan',type=str,default='None',help='Rentang Scanning dalam format: Titik1,Titik2,JumlahTitik. Contoh:2.5,1.0,100.')
 # Input untuk perhitungan NEB
 parser.add_argument('-produk','--produk',type=str,help='Struktur produk yang digunakan dalam interpolasi NEB dalam format koordinat Cartesian.')
-parser.add_argument('-trans','--transitionstate',type=str,help='Struktur perkiraan keadaan transisi yang digunakan dalam format koordinat Cartesian.')
+parser.add_argument('-trans','--transitionstate',default='None',type=str,help='Struktur perkiraan keadaan transisi yang digunakan dalam format koordinat Cartesian.')
 # Input untuk IRC
 parser.add_argument('-irciter','--irciter',type=int,default=20,help='Iterasi maksimum IRC Orca.')
 parser.add_argument('-printlevel','--printlevel',type=str,default='1',help='Print level dalam IRC Orca. Default=1')
@@ -212,7 +212,7 @@ obabel geom.smi -O geom.xyz --gen3d""".format(opt.nproc),file=fout)
     geom = 'geom.xyz'
 ### ORCA
 if opt.software == 'orca':
-    orca(opt.job,opt.method,opt.nproc,geom,opt.charge,opt.mult,opt.scalefreq,opt.temp,opt.pressure,opt.nroots,opt.tda,opt.solvent,opt.constraints,opt.qmatoms,opt.totalcharge,opt.totalmult,opt.qm2method,opt.qm2basis,opt.activeatoms,opt.hessfile,opt.dispersion,opt.aim,opt.produk,opt.transitionstate,opt.irciter,opt.printlevel, opt.inithess,opt.grid, opt.finalgrid)
+    orca(opt.job,opt.method,opt.nproc,geom,opt.charge,opt.mult,opt.scalefreq,opt.temp,opt.pressure,opt.nroots,opt.tda,opt.solvent,opt.constraints,opt.qmatoms,opt.totalcharge,opt.totalmult,opt.qm2method,opt.qm2basis,opt.activeatoms,opt.hessfile,opt.dispersion,opt.aim,opt.produk,opt.transitionstate,opt.irciter,opt.printlevel, opt.inithess,opt.grid, opt.finalgrid,opt.iter)
 
 ### NWChem
 if opt.software == 'nwchem':
@@ -400,4 +400,4 @@ if opt.job == 'ligprep' and opt.software == 'gmx':
 
 # Program XTB Standalone
 if opt.software == 'xtb':
-	xtb(opt.job,geom,opt.nproc,opt.produk,opt.temp,opt.nrun,opt.npoint,opt.anopt,opt.kpush,opt.kpull,opt.ppull,opt.alp,opt.distance,opt.angle,opt.dihedral,opt.scanmode,opt.iter,opt.scan)
+	xtb(opt.job,geom,opt.nproc,opt.produk,opt.temp,opt.nrun,opt.npoint,opt.anopt,opt.kpush,opt.kpull,opt.ppull,opt.alp,opt.distance,opt.angle,opt.dihedral,opt.scanmode,opt.iter,opt.scan,opt.solvent)

lib/cmmde_orca.py

@@ -1,4 +1,4 @@
-def orca(job,method,nproc,geom,charge,mult,scalfreq,temperature,pressure,nroots,tda,solvent,constraints,qmatoms,totalcharge,totalmult,qm2method,qm2basis,activeatoms,hessfile,disp,aim,product,ts,irciter, printlevel, inithess,grid, finalgrid):
+def orca(job,method,nproc,geom,charge,mult,scalfreq,temperature,pressure,nroots,tda,solvent,constraints,qmatoms,totalcharge,totalmult,qm2method,qm2basis,activeatoms,hessfile,disp,aim,product,ts,irciter, printlevel, inithess,grid, finalgrid,maxiter):
     if 'opt' in job or 'Opt' in job or 'OPT' in job and not 'ts' in job: 
         method += ' opt'
     if 'freq' in job and ('XTB2' in method or 'XTB' in method):
@@ -8,7 +8,7 @@ def orca(job,method,nproc,geom,charge,mult,scalfreq,temperature,pressure,nroots,
     if 'ts' in job and 'neb' not in job:
         method += ' OptTS'
     if 'neb-ts' in job:
-        method += ' NEB-TS Freq'
+        method += ' NEB-TS'
     if 'neb' in job and 'ts' not in job:
         method += ' NEB'
     if 'neb-ci' in job:
@@ -30,6 +30,10 @@ def orca(job,method,nproc,geom,charge,mult,scalfreq,temperature,pressure,nroots,
         print("""%pal 
  nprocs {} 
 end""".format(nproc),file=f)
+        if 'opt' in job:
+        	print("""%geom
+  maxiter {}
+end""".format(maxiter))
         if qmatoms != 'None':
             print("""%qmmm
    QMAtoms {{ {} }} end
@@ -50,10 +54,10 @@ end""".format(nproc),file=f)
             print("end",file=f)
         if hessfile != 'None':
             print("""%geom
-    MaxIter 10000
+    MaxIter {}
     InHess Read
     InHessName "{}"
-end""".format(hessfile),file=f)
+end""".format(maxiter,hessfile),file=f)
         # Baris koordinat atom
         print("""     
 *xyzfile {} {} {}
@@ -71,10 +75,16 @@ end""".format(scalfreq,temperature,pressure),file=f)
   tda {}
 end""".format(nroots,tda),file=f)
         if 'neb' in job:
-            print("""%NEB
-NEB_END_XYZFILE "{}"
-NEB_TS_XYZFILE "{}"
-END""".format(product,ts),file=f)     
+        	print("""%geom 
+  maxiter {}
+end""".format(maxiter),file=f)
+        	print("""%NEB
+  neb_end_xyzfile "{}" """.format(product),file=f)
+        	if ts != 'None':
+        		print("""  neb_ts_xyzfile "{}"
+end""".format(ts),file=f)
+        	else:
+        		print("end",file=f)     
         if 'irc' in job:
             print("""%irc
   MaxIter {}

lib/cmmde_xtb.py

@@ -1,6 +1,6 @@
 # CMMDE function for xTB standalone program
 import os
-def xtb(job,geom,nproc,product,temperature,nrun,npoint,anopt,kpush,kpull,ppull,alp,distance,angle,dihedral,scanmode,maxiter,scan):
+def xtb(job,geom,nproc,product,temperature,nrun,npoint,anopt,kpush,kpull,ppull,alp,distance,angle,dihedral,scanmode,maxiter,scan,solvent):
 	with open('run.sh','w') as fout:
 		print("""#!/bin/bash
 #SBATCH --nodes=1
@@ -10,15 +10,30 @@ def xtb(job,geom,nproc,product,temperature,nrun,npoint,anopt,kpush,kpull,ppull,a
 export OMP_NUM_THREADS={}
 cd $PWD""".format(nproc),file=fout)
 		if 'opt' in job:
-			print("$XTB_COMMAND {} --opt -P {} > xtb.out".format(geom,nproc),file=fout)
+			if solvent != 'none':
+				print("$XTB_COMMAND {} --opt -P {} --alpb {} > xtb.out".format(geom,nproc,solvent),file=fout)
+			else:
+				print("$XTB_COMMAND {} --opt -P {} > xtb.out".format(geom,nproc),file=fout)
 		if 'freq' in job:
-			print("$XTB_COMMAND {} --hess -P {} --input cmmd.in > xtb.out".format(geom,nproc), file=fout)
+			if solvent != 'none':
+				print("$XTB_COMMAND {} --hess -P {} --input cmmd.in --alpb {} > xtb.out".format(geom,nproc,solvent), file=fout)
+			else:
+				print("$XTB_COMMAND {} --hess -P {} --input cmmd.in > xtb.out".format(geom,nproc), file=fout)
 		if 'opt' in job and 'freq' in job:
-			print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in > xtb.out".format(geom,nproc),file=fout)
+			if solvent != 'none':
+				print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in --alpb {} > xtb.out".format(geom,nproc,solvent),file=fout)
+			else:	
+				print("$XTB_COMMAND {} --ohess -P {} --input cmmd.in > xtb.out".format(geom,nproc),file=fout)
 		if 'path' in job:
-			print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} > xtb.out".format(geom,product,nproc),file=fout)
+			if solvent != 'none':
+				print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} --alpb {} > xtb.out".format(geom,product,nproc,solvent),file=fout)
+			else:	
+				print("$XTB_COMMAND {} --path {} --input cmmd.in -P {} > xtb.out".format(geom,product,nproc),file=fout)
 		if 'scan' in job:
-			print("$XTB_COMMAND {} --opt -P {} --input cmmd.in > xtb.out".format(geom,nproc), file=fout)
+			if solvent != 'none':
+				print("$XTB_COMMAND {} --opt -P {} --input cmmd.in --alpb {} > xtb.out".format(geom,nproc,solvent), file=fout)
+			else:	
+				print("$XTB_COMMAND {} --opt -P {} --input cmmd.in > xtb.out".format(geom,nproc), file=fout)
 	if 'freq' in job:
 		with open('cmmd.in', 'w') as f:
 			print("""$thermo
@@ -57,3 +72,4 @@ $end""".format(nrun,npoint,anopt,kpush,kpull,ppull,alp),file=f)
 
 	os.system('sbatch run.sh')
 	
+