CMMDE/lib/cmmde_orca.py

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,solvtype,cpcmsurface,draco,draco_charges,solvator,nsolv,solventfile,solvprint,randomsolv,fixsolute,use_eeq,droplet,droplet_radius,guest,guestcharge,docklevel,nrepeatguest,cumulativeguest,fixhost,evpes,nopt,no_opt,goat_iter,goat_opt_iter,skip_initopt,randomseed,readensemble,autowall,mintemplist,nworkers,maxitermult,keepworker,worker_randstart,uphill_atoms,gfn_uphill,align,en_diff,max_en,max_entropy,conf_temp,min_delta_S,conf_degen,free_heteroatoms,free_nonh_atoms,free_fragments,freeze_bonds,freeze_angles,freeze_cistrans,freeze_amides,maxcoordnum,max_topo_diff):
    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 and 'neb' not in job:
        method += ' OptTS'
    if 'neb-ts' in job:
        method += ' NEB-TS'
    if 'neb' in job and 'ts' not in job:
        method += ' NEB'
    if 'neb-ci' in job:
        method += ' NEB-CI'
    if 'freq' in job and ('XTB2' not in method and 'XTB' not in method and 'XTBFF' not in method):
        method += ' freq'
    if disp != 'None':
        method += ' {}'.format(disp)
    if aim == 'true' or aim == 'True' or aim == 'TRUE':
        method += ' AIM'
    if solvent != 'none' and ('XTB2' in method or 'XTB' in method or 'XTBFF' in method or 'GFNFF' in method or 'GFN0XTB' in method or 'GFN1XTB' in method or 'GFN2XTB' in method):
        method += ' ALPB({})'.format(solvent)
        if solvtype == 'GBSA':
            method += ' GBSA({})'.format(solvent)
    if solvent != 'none' and ('XTB2' not in method and 'XTB' not in method and 'XTBFF' not in method and 'GFNFF' not in method and 'GFN0XTB' not in method and 'GFN1XTB' not in method and 'GFN2XTB' not in method):
        if draco == True:
            method += ' DRACO'
        if solvtype == 'CPCM' or solvtype == 'cpcm':
            method += ' CPCM({})'.format(solvent)
        elif solvtype == 'CPCMC' or solvtype == 'COSMO' or solvtype == 'cosmo':
            method += ' CPCMC({})'.format(solvent)
        elif solvtype == 'SMD' or solvtype == 'smd':
            method += ' SMD({})'.format(solvent)
    
    if job == 'goat' or job == 'GOAT':
        method += ' GOAT'
    if job == 'goat-react' or job == 'GOAT-REACT':
        method += ' GOAT-REACT'
    if job == 'goat-explore' or job == 'GOAT-EXPLORE':
        method += ' GOAT-EXPLORE'

    with open('cmmd.in','w') as f:
        print("#CMMDE generated Orca input file", file=f)
        print("!{}".format(method), file=f)
        print("""%pal 
 nprocs {} 
end""".format(nproc),file=f)
        if 'opt' in job:
        	print("""%geom
  maxiter {}
end""".format(maxiter),file=f)
        if qmatoms != 'None':
            print("""%qmmm
   QMAtoms {{ {} }} end
   Charge_Total {}
   Mult_Total {}""".format(qmatoms,totalcharge,totalmult),file=f)
            if qm2method != 'None':
                print("""   QM2CUSTOMMETHOD "{}"
   QM2CUSTOMBASIS "{}" """.format(qm2method,qm2basis),file=f)
            if activeatoms != 'None':
                print("ActiveAtoms {} end".format(activeatoms))
            print("end",file=f)
        if constraints != 'None':
            print("%geom", file=f)
            print("Constraints",file=f)
            for i in constraints.split(','):
                print("""{{ {} }}""".format(i),file=f)
            print("end",file=f)
            print("end",file=f)
        if hessfile != 'None':
            print("""%geom
    MaxIter {}
    InHess Read
    InHessName "{}"
end""".format(maxiter,hessfile),file=f)
        # Baris koordinat atom
        print("""     
*xyzfile {} {} {}
""".format(charge,mult,geom)
        , file=f)
        if 'freq' in job:
            print("""%freq 
 scalfreq {} 
 Temp {}
 Pressure {}
end""".format(scalfreq,temperature,pressure),file=f)
        if 'td' in job:
            print("""%tddft 
  nroots {}
  tda {}
end""".format(nroots,tda),file=f)
        if 'neb' in job:
        	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 {}
  PrintLevel {}
  InitHess {}
  Hess_filename "{}"
end

%method
  Grid {}
  FinalGrid {}
end
""".format(irciter, printlevel, inithess, hessfile, grid, finalgrid),file=f)
        if solvent != 'none' and 'XTB' not in method:
            print('%CPCM',file=f)
            if cpcmsurface == 'SES' or cpcmsurface == 'ses':
                print('SURFACETYPE GEPOL_SES_GAUSSIAN',file=f)
            else:
                print('SURFACETYPE VDW_GAUSSIAN',file=f)
            if draco == True:
                if draco_charges == 'ceh' or draco_charges == 'CEH':
                    print('draco_charges ceh',file=f)
                else:
                    print('draco_charges eeq',file=f)
            print('END',file=f) 
        if solvator == True:
            print('%SOLVATOR',file=f)
            print('  NSOLV {}'.format(nsolv),file=f)
            print('  CLUSTERMODE STOCHASTIC',file=f)
            if solventfile != 'none':
                print("""  SOLVENTFILE "{}" """.format(solventfile),file=f)
            print('  PRINTLEVEL {}'.format(solvprint),file=f)
            print('  RANDOMSOLV {}'.format(randomsolv),file=f)
            print('  FIXSOLUTE {}'.format(fixsolute),file=f)
            print('  USEEEQCHARGES {}'.format(use_eeq),file=f)
            print('  DROPLET {}'.format(droplet),file=f)
            if droplet == 'True' or droplet == 'true' or droplet == 'TRUE':
                print('  RADIUS {}'.format(droplet_radius),file=f)
            print('END',file=f)
        if 'docker' in job:
            print('%DOCKER',file=f)
            print("""  GUEST "{}" """.format(guest),file=f)
            print('  GuestCharge {}'.format(guestcharge))
            print('  DOCKLEVEL {}'.format(docklevel),file=f)
            print('  NREPEATGUEST {}'.format(nrepeatguest),file=f)
            print('  CUMULATIVE {}'.format(cumulativeguest),file=f)
            print('  FIXHOST {}'.format(fixhost),file=f)
            print('  EVPES {}'.format(evpes),file=f)
            print('  NOPT {}'.format(nopt),file=f)
            print('  NOOPT {}'.format(no_opt),file=f)
            print('END',file=f)
        if 'GOAT' in job or 'goat' in job:
            print('%GOAT',file=f)
            print('  MAXITER {}'.format(goat_iter),file=f)
            print('  MAXOPTITER {}'.format(goat_opt_iter),file=f)
            print('  SKIPINITIALOPT {}'.format(skip_initopt),file=f)
            print('  RANDOMSEED {}'.format(randomseed),file=f)
            if readensemble != 'none':
                print('  READENSEMBLE {}'.format(readensemble),file=f)
            print('  AUTOWALL {}'.format(autowall),file=f)
            if mintemplist != 'none':
                print('  MINTEMPLIST {}'.format(mintemplist),file=f)
            print('  NWORKERS {}'.format(nworkers),file=f)
            if maxitermult != 'none':
                print('  MAXITERMULT {}'.format(maxitermult),file=f)
            print('  KEEPWORKERDATA {}'.format(keepworker),file=f)
            print('  WORKERRANDOMSTART {}'.format(worker_randstart),file=f)
            if uphill_atoms != 'none':
                print('  UPHILLATOMS {} END'.format(uphill_atoms),file=f)
            print('  GFNUPHILL {}'.format(gfn_uphill),file=f)
            print('  ALIGN {}'.format(align),file=f)
            print('  ENDIFF {}'.format(en_diff),file=f)
            print('  MAXEN {}'.format(max_en),file=f)
           # if 'EXPLORE' in job or 'Explore' in job or 'explore' in job:
           #     print('  RMSDMETRIC EIGENVALUE',file=f)
            #else: 
             #   print('  RMSDMETRIC RMSD',file=f)
            if max_entropy == 'True':
                print('  MAXENTROPY {}'.format(max_entropy),file=f)
                print('  CONFTEMP {}'.format(conf_temp),file=f)
                print('  MINDELS {}'.format(min_delta_S),file=f)
            print('  CONFDEGEN {}'.format(conf_degen),file=f)
            print('  FREEHETEROATOMS {}'.format(free_heteroatoms),file=f)
            print('  FREENONHATOMS {}'.format(free_nonh_atoms),file=f)
            print('  FREEFRAGMENTS {}'.format(free_fragments),file=f)
            print('  FREEZEBONDS {}'.format(freeze_bonds),file=f)
            print('  FREEZEANGLES {}'.format(freeze_angles),file=f)
            print('  FREEZECISTRANS {}'.format(freeze_cistrans),file=f)
            print('  FREEZEAMIDES {}'.format(freeze_amides),file=f)
            if maxcoordnum != 'none':
                print('  MAXCOORDNUMBER {}'.format(maxcoordnum),file=f)
            if max_topo_diff != 'none':
                print('  MAXTOPODIFF {}'.format(max_topo_diff),file=f)
            print('END',file=f)
    return