Fix the cmmde_solution

Aditya Wibawa Sakti 2 years ago
parent 4fb3a00ab6
commit d4be395790
  1. 4
      bin/cmmde.py
  2. BIN
      lib/__pycache__/cmmde_hubbard.cpython-39.pyc
  3. BIN
      lib/__pycache__/cmmde_orca.cpython-39.pyc
  4. 2
      lib/cmmde_hubbard.py
  5. 16
      lib/cmmde_orca.py
  6. 43
      lib/cmmde_solution.py

@ -60,6 +60,8 @@ parser.add_argument('-l', '--lapang', type=float, default=5, help='Panjang tamba
parser.add_argument('-gen','--generate_dftbinp',type=str,default='false',help='Apakah ingin mengkonversi ke dalam format koordinat xyz?')
parser.add_argument('-mp', '--pelarut', type=str, help='Nama file molekul pelarut dalam format .xyz (ditulis tanpa ekstensi).')
parser.add_argument('-nequil','--nequil',type=int, default=50000, help='Jumlah step pada saat ekuilibrasi.')
parser.add_argument('-nnpt','--nnpt',type=int, default=50000, help='Jumlah step pada saat ekuilibrasi NPT.')
parser.add_argument('-comp','--compress',type=float, default=4.5e-6, help='Nilai kompresibilitas. Default=4.5e-6.')
parser.add_argument('-nprod','--nprod',type=int, default=400000, help='Jumlah step pada saat production.')
parser.add_argument('-prod', '--production', type=str, default='None', help='Ensembel yang digunakan dalam production run. Pilihan:nve,npt,nvt.')
parser.add_argument('-cp', '--c_pelarut', type=int, default=0, help='Muatan bersih molekul pelarut')
@ -373,7 +375,7 @@ if opt.software == 'gromacs':
#SBATCH --time=168:0:0
export OMP_NUM_THREADS={}
cd $PWD
$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {}""".format(opt.nproc, opt.terlarut,opt.pelarut,opt.c_terlarut,opt.persen_terlarut,opt.persen_pelarut,opt.lapang,opt.cation,opt.generate_dftbinp,opt.NumPelarut,opt.production,opt.nprod,opt.nequil,opt.deltat,opt.charge_type),file=fout)
$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {} -nnpt {} -comp {}""".format(opt.nproc, opt.terlarut,opt.pelarut,opt.c_terlarut,opt.persen_terlarut,opt.persen_pelarut,opt.lapang,opt.cation,opt.generate_dftbinp,opt.NumPelarut,opt.production,opt.nprod,opt.nequil,opt.deltat,opt.charge_type,opt.nnpt,opt.compress),file=fout)
os.system('sbatch run.sh')
if opt.job == 'proprep' and opt.software == 'gmx':

@ -19,6 +19,8 @@ def azimuth(element):
'B' : '2',
'Au' : '3',
'Rh' : '3',
'Ni' : '3',
'Co' : '3',
'Ti' : '3',
'C' : '2'
}

@ -5,10 +5,14 @@ def orca(job,method,nproc,geom,charge,mult,scalfreq,temperature,pressure,nroots,
method += ' Numfreq'
if 'irc' in job:
method += ' IRC'
if 'ts' in job:
if 'ts' in job and 'neb' not in job:
method += ' OptTS'
if 'NEB-TS' in job:
method += ' NEB-TS'
if 'neb-ts' in job:
method += ' NEB-TS Freq'
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':
@ -66,10 +70,10 @@ end""".format(scalfreq,temperature,pressure),file=f)
nroots {}
tda {}
end""".format(nroots,tda),file=f)
if 'NEB' in job:
if 'neb' in job:
print("""%NEB
NEB_END_XYZFILE {}
NEB_TS_XYZFILE {}
NEB_END_XYZFILE "{}"
NEB_TS_XYZFILE "{}"
END""".format(product,ts),file=f)
if 'irc' in job:
print("""%irc

@ -22,20 +22,23 @@ parser.add_argument('-cat','--cation',type=str, default='none',help='Kation yang
parser.add_argument('-p', '--pressure', default=1.0, type=float, help='Tekanan dalam satuan bar')
parser.add_argument('-t', '--temperature', default=298.15, type=float, help='Suhu yang digunakan dalam simulasi.')
parser.add_argument('-nequil','--nequil',type=int, default=50000, help='Jumlah step pada saat ekuilibrasi.')
parser.add_argument('-nnpt','--nnpt',type=int, default=50000, help='Jumlah step pada saat ekuilibrasi NPT.')
parser.add_argument('-nprod','--nprod',type=int, default=400000, help='Jumlah step pada saat production.')
parser.add_argument('-dt','--dt',type=float, default=1, help='Step simulasi dinamika molekul yang dilakukan.')
parser.add_argument('-comp','--compress',type=float, default=4.5e-6, help='Nilai kompresibilitas. Default=4.5e-6.')
parser.add_argument('--packmol', type=str, default='/home/adit/opt/oldpackmol/packmol')
parser.add_argument('-l','--lapang',type=float, default=5, help='Ruang lapang untuk atom-atom bergerak di dalam kotak larutan (angstrom).')
parser.add_argument('-gen','--generate_dftbinp',type=str,default='false',help='Apakah ingin mengkonversi ke dalam format koordinat xyz?')
parser.add_argument('-prod','--production',type=str,default='None',help='Jenis production run yang ingin dilakukan. Pilihan: NPT (recommended), NVE, dan NVT.')
opt=parser.parse_args(sys.argv[1:])
# Input file minimisasi energi dalam GROMACS
minim_mdp = """
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 100.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
integrator = cg ; Algorithm (steep or cg)
emtol = 1 ; Stop minimization when the maximum force < 1 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
@ -50,7 +53,7 @@ pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
"""
nve_mdp = """
define = -DFLEXIBLE
integrator = md ; leap-frog integrator
integrator = md
nsteps = {} ; 1 * 500000 = 50 ps
dt = 0.001 ; 0.5 fs
nstxout = 100 ; save coordinates every 1.0 ps
@ -81,21 +84,21 @@ pcoupl = no ; no pressure coupling in NVE
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = no ; Velocity generation is off
gen_vel = yes ; Velocity generation is off
"""
# Input file simulasi menggunakan ensembel kanonik (NVT) dalam GROMACS
nvt_mdp="""
define = -DFLEXIBLE
integrator = md ; leap-frog integrator
nsteps = {} ; 1 * 500000 = 50 ps
nsteps = {}
dt = 0.001 ; 1 fs
nstxout = 100 ; save coordinates every 1.0 ps
;nstenergy = 100 ; save energies every 1.0 ps
;nstlog = 100 ; update log file every 1.0 ps
; Bond parameters
continuation = no ; first dynamics run
continuation = yes ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
@ -114,16 +117,14 @@ fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = System ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
tau_t = 0.01 ; time constant, in ps
ref_t = {} ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = {} ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
gen_vel = no ; assign velocities from Maxwell distribution
"""
# Input file simulasi isoterm-isobarik (NPT) dalam GROMACS. Harapannya, setelah dilakukan NPT, akan diperoleh sistem dengan massa jenis yang optimal.
@ -131,8 +132,8 @@ npt_mdp = """
title = NPT equilibration
; Run parameters
integrator = md ; leap-frog integrator
nsteps = {} ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
nsteps = {}
dt = 0.001 ; 1 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
@ -143,7 +144,7 @@ continuation = yes ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
lincs_order = 6 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
@ -162,9 +163,9 @@ ref_t = {} ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Berendsen ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
tau_p = 2 ; time constant, in ps
ref_p = {} ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
compressibility = {} ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
@ -205,9 +206,9 @@ ref_t = {} ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Berendsen ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
tau_p = 10 ; time constant, in ps
compressibility = {} ; isothermal compressibility of water, bar^-1
ref_p = {} ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
@ -556,16 +557,18 @@ quit""",file=fout)
# Menuliskan semua input file yang dibutuhkan, meliputi simulasi NVE, NVT, dan NPT
nequil = opt.nequil
nnpt = opt.nnpt
nprod = opt.nprod
compress = opt.compress
with open('minim.mdp', 'w') as f:
print(minim_mdp.format(half_box, half_box), file=f)
with open('nve.mdp', 'w') as f:
print(nve_mdp.format(nequil,half_box,half_box), file=f)
with open('nvt.mdp', 'w') as f:
print(nvt_mdp.format(nequil,half_box, half_box,temperature,temperature), file=f)
print(nvt_mdp.format(nequil,half_box, half_box,temperature), file=f)
with open('npt.mdp', 'w') as f:
print(npt_mdp.format(nequil,half_box, half_box,temperature,pressure), file=f)
print(npt_mdp.format(nnpt,half_box, half_box,temperature,pressure,compress), file=f)
gmxscript.grompp(f="minim.mdp", c="system_box.pdb", o="mini.tpr", p="system_GMX.top", maxwarn=2)
gmxscript.mdrun(deffnm="mini",ntmpi=1)
@ -579,7 +582,7 @@ quit""",file=fout)
if prod == 'npt':
with open('nptp.mdp', 'w') as f:
print(nptp_mdp.format(nprod,opt.dt/2000,half_box,half_box,temperature,pressure), file=f)
print(nptp_mdp.format(nprod,opt.dt/2000,half_box,half_box,temperature,compress,pressure), file=f)
gmxscript.grompp(f="nptp.mdp", c="npt.gro", p="system_GMX.top", o="nptp.tpr",maxwarn=2)
gmxscript.mdrun(deffnm="nptp", v=True, ntmpi=1)
gmxscript.trjconv(f="nptp.trr", s="nptp.tpr", n="mini.ndx", o="finalsystem.pdb")

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