add IRC

bin/cmmde.py

@@ -111,6 +111,17 @@ parser.add_argument('-nlig','--nligands',type=int,help='Jumlah ligan yang akan d
 parser.add_argument('-solvent','--solvent',type=str,default='none',help='Pelarut yang digunakan dalam perhitungan.')
 # Input untuk simulasi MD sistem protein
 parser.add_argument('-protein','--protein',type=str,help='Struktur protein dalam format pdb')
+# 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.')
+# 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')
+parser.add_argument('-inithess','--inithess',type=str,default='Read',help='Cara menginisiasi Hessian. Default: Read.')
+parser.add_argument('-grid','--grid',type=int,default=2,help='Ukuran grid dalam integrasi Orca.')
+parser.add_argument('-finalgrid','--finalgrid',type=int,default=4,help='Ukuran final grid dalam integrasi Orca.')
+
+
 # Input untuk perhitungan bergantung waktu
 parser.add_argument('-nr','--nroots',type=int,default=5,help='Jumlah orbital aktif yang diperhitungkan dalam perhitungan bergantung waktu.')
 parser.add_argument('-tda','--tda',type=str,default='false',help='Apakah akan digunakan pendekatan Tamm-Dancoff. Default = false.')
@@ -184,7 +195,7 @@ 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)
+    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)
 
 ### NWChem
 if opt.software == 'nwchem':

lib/cmmde_orca.py

@@ -1,10 +1,14 @@
-def orca(job,method,nproc,geom,charge,mult,scalfreq,temperature,pressure,nroots,tda,solvent,constraints,qmatoms,totalcharge,totalmult,qm2method,qm2basis,activeatoms,hessfile,disp,aim):
+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):
-    if 'opt' in job or 'Opt' in job or 'OPT' in job: 
+    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):
         method += ' Numfreq'
+    if 'irc' in job:
+        method += ' IRC'
     if 'ts' in job:
         method += ' OptTS'
+    if 'NEB-TS' in job:
+        method += ' NEB-TS'
     if 'freq' in job and ('XTB2' not in method and 'XTB' not in method and 'XTBFF' not in method):
         method += ' freq'
     if disp != 'None':
@@ -62,5 +66,23 @@ end""".format(scalfreq,temperature,pressure),file=f)
   nroots {}
   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)     
+        if 'irc' in job:
+            print("""%irc
+  MaxIter {}
+  PrintLevel {}
+  InitHess {}
+  Hess_filename "{}"
+end
+
+%method
+  Grid {}
+  FinalGrid {}
+end
+""".format(irciter, printlevel, inithess, hessfile, grid, finalgrid),file=f)
     return