added non-slurm calculations

2 years ago · 500f7c3fd1
parent 64a32ccbc6
commit 500f7c3fd1
14 changed files with 177 additions and 89 deletions
--- a/.DS_Store
+++ b/.DS_Store
--- a/bin/cmmde.py
+++ b/bin/cmmde.py
@ -28,7 +28,7 @@ parser.add_argument('-m','--method',type=str,default='XTB2',help='Metode yang di
 parser.add_argument('-sfreq','--scalefreq',type=float,default=1, help='Faktor skala frekuensi yang digunakan.')
 # 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/external/slakos/origin/3ob-3-1',help='Lokasi folder berisikan himpunan parameter DFTB yang akan digunakan.')
+parser.add_argument('-para','--parapath',type=str,default='/Users/adit/opt/dftbplus/external/slakos/origin/3ob-3-1',help='Lokasi folder berisikan himpunan parameter DFTB yang akan digunakan.')
 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')
@ -180,6 +180,7 @@ parser.add_argument('-cpress','--cellpress',type=float,default=0.0,help='Tekanan
 parser.add_argument('-press_conv','--press_conv_thr',type=float,default=0.5,help='Kriteria konvergensi untuk tekanan sel. Default=0.5 kbar.')
 parser.add_argument('-nband','--nband',type=int,default=8,help='Jumlah tingkat energi yang ingin diplot dalam DOS.')
 parser.add_argument('-occ','--occ',type=str,default='tetrahedra',help='Metode smearing yang digunakan. Default: tetrahedra. Pilihan: smearing, tetrahedra_lin, tetrahedra_opt, fixed, from_input.')
+parser.add_argument("-slurm","--slurm",type=str,default="true",help="Apakah akan menggunakan slurm atau tidak. Default: true")

 opt=parser.parse_args(sys.argv[1:])

@ -187,8 +188,9 @@ opt=parser.parse_args(sys.argv[1:])
 if ('.xyz' or '.pdb' or 'POSCAR' or '.vasp' or '.poscar') in opt.input:
    geom = opt.input
 elif '.mol2' in opt.input:
-    with open('run_babel.sh','w') as fout:
-        print("""#!/bin/bash
+    if opt.slurm == "true":
+        with open('run_babel.sh','w') as fout:
+            print("""#!/bin/bash
 #SBATCH --nodes=1
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=1
@ -196,20 +198,37 @@ elif '.mol2' in opt.input:
 export OMP_NUM_THREADS={}
 cd $PWD
 obabel {} -O geom.xyz""".format(opt.nproc,opt.input),file=fout)
-    os.system('sbatch run_babel.sh')
+        os.system('sbatch run_babel.sh')
+    else:
+        with open('run_babel.sh','w') as fout:
+            print("""#!/bin/bash
+export OMP_NUM_THREADS={}
+cd $PWD
+obabel {} -O geom.xyz""".format(opt.nproc,opt.input),file=fout)
+        os.system("chmod +x run_babel.sh")
+        os.system('./run_babel.sh')
    geom = 'geom.xyz'
 elif ('.mol2' not in opt.input and '.xyz' not in opt.input and '.pdb' not in opt.input and '.vasp' not in opt.input and '.poscar' not in opt.input and 'POSCAR' not in opt.input and '.gen' not in opt.input):
    os.system("echo '{}' > geom.smi".format(opt.input))
-    with open('run_babel.sh','w') as fout:
-        print("""#!/bin/bash
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --time=168:0:0
-export OMP_NUM_THREADS={}
-cd $PWD
-obabel geom.smi -O geom.xyz --gen3d""".format(opt.nproc),file=fout)
-    os.system('sbatch run_babel.sh')
+    if opt.slurm == "true":
+        with open('run_babel.sh','w') as fout:
+            print("""#!/bin/bash
+    #SBATCH --nodes=1
+    #SBATCH --ntasks=1
+    #SBATCH --cpus-per-task=1
+    #SBATCH --time=168:0:0
+    export OMP_NUM_THREADS={}
+    cd $PWD
+    obabel geom.smi -O geom.xyz --gen3d""".format(opt.nproc),file=fout)
+        os.system('sbatch run_babel.sh')
+    else:
+        with open('run_babel.sh','w') as fout:
+            print("""#!/bin/bash
+    export OMP_NUM_THREADS={}
+    cd $PWD
+    obabel geom.smi -O geom.xyz --gen3d""".format(opt.nproc),file=fout)
+        os.system("chmod +x run_babel.sh")
+        os.system('./run_babel.sh')
    while not os.path.exists('geom.xyz'):
        time.sleep(3)
    geom = 'geom.xyz'
@ -236,6 +255,7 @@ if opt.software == 'dock':
        addcharge(opt.input,opt.chargetype)
    if opt.job == 'sphgen':
        sphgen(opt.input)
+    if opt.slurm == 'true':
        with open('run_sphgen.sh','w') as fout:
            print("""#!/bin/bash
 #SBATCH --nodes=1
@ -247,46 +267,81 @@ cd $PWD
 $DOCK_DIR/sphgen
 $DOCK_DIR/sphere_selector protein.sph {} {}""".format(opt.nproc,opt.ligand,opt.dockrange),file=fout)
        os.system("sbatch run_sphgen.sh")
-
+    else:
+        with open('run_sphgen.sh','w') as fout:
+            print("""#!/bin/bash
+export OMP_NUM_THREADS={}
+cd $PWD
+$DOCK_DIR/sphgen
+$DOCK_DIR/sphere_selector protein.sph {} {}""".format(opt.nproc,opt.ligand,opt.dockrange),file=fout)
+        os.system("chmod +x run_sphgen.sh")
+        os.system("./run_sphgen.sh")
    if opt.job == 'showsphere':
        showsphere()
    if opt.job == 'gridgen':
        gridgen(opt.input)
-        with open('run_grid.sh','w') as fout:
-            print("""#!/bin/bash
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --time=168:0:0
-export OMP_NUM_THREADS={}
-cd $PWD
-$DOCK_DIR/grid -i grid.in""".format(opt.nproc),file=fout)
-        os.system("sbatch run_grid.sh")
-
+        if opt.slurm == "true":
+            with open('run_grid.sh','w') as fout:
+                print("""#!/bin/bash
+    #SBATCH --nodes=1
+    #SBATCH --ntasks=1
+    #SBATCH --cpus-per-task=1
+    #SBATCH --time=168:0:0
+    export OMP_NUM_THREADS={}
+    cd $PWD
+    $DOCK_DIR/grid -i grid.in""".format(opt.nproc),file=fout)
+            os.system("sbatch run_grid.sh")
+        else:
+            with open('run_grid.sh','w') as fout:
+                print("""#!/bin/bash
+    export OMP_NUM_THREADS={}
+    cd $PWD
+    $DOCK_DIR/grid -i grid.in""".format(opt.nproc),file=fout)
+            os.system("chmod +x run_grid.sh")
+            os.system("./run_grid.sh")
+    
    if opt.job == 'rigiddock':
        rigiddock(opt.ligand,opt.calcrmsd)
-        with open('run_rigiddock.sh','w') as fout:
-            print("""#!/bin/bash
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --time=168:0:0
-export OMP_NUM_THREADS={}
-cd $PWD
-$DOCK_DIR/dock6 -i rigid.in -o rigid.out""".format(opt.nproc),file=fout)
-        os.system("sbatch run_rigiddock.sh")
+        if opt.slurm == "true":
+            with open('run_rigiddock.sh','w') as fout:
+                print("""#!/bin/bash
+    #SBATCH --nodes=1
+    #SBATCH --ntasks=1
+    #SBATCH --cpus-per-task=1
+    #SBATCH --time=168:0:0
+    export OMP_NUM_THREADS={}
+    cd $PWD
+    $DOCK_DIR/dock6 -i rigid.in -o rigid.out""".format(opt.nproc),file=fout)
+            os.system("sbatch run_rigiddock.sh")
+        else:
+            with open('run_rigiddock.sh','w') as fout:
+                print("""#!/bin/bash
+    export OMP_NUM_THREADS={}
+    cd $PWD
+    $DOCK_DIR/dock6 -i rigid.in -o rigid.out""".format(opt.nproc),file=fout)
+            os.system("chmod +x run_rigiddock.sh")
+            os.system("./run_rigiddock.sh")
    if opt.job == 'flexdock':
        flexdock(opt.ligand,opt.calcrmsd)
-        with open('run_flexdock.sh','w') as fout:
-            print("""#!/bin/bash
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --time=168:0:0
-export OMP_NUM_THREADS={}
-cd $PWD
-$DOCK_DIR/dock6 -i flex.in -o flex.out""".format(opt.nproc),file=fout)
-        os.system("sbatch run_flexdock.sh")
+        if opt.slurm == "true":
+            with open('run_flexdock.sh','w') as fout:
+                print("""#!/bin/bash
+    #SBATCH --nodes=1
+    #SBATCH --ntasks=1
+    #SBATCH --cpus-per-task=1
+    #SBATCH --time=168:0:0
+    export OMP_NUM_THREADS={}
+    cd $PWD
+    $DOCK_DIR/dock6 -i flex.in -o flex.out""".format(opt.nproc),file=fout)
+            os.system("sbatch run_flexdock.sh")
+        else:
+            with open('run_flexdock.sh','w') as fout:
+                print("""#!/bin/bash
+    export OMP_NUM_THREADS={}
+    cd $PWD
+    $DOCK_DIR/dock6 -i flex.in -o flex.out""".format(opt.nproc),file=fout)
+            os.system("chmod +x run_flexdock.sh")
+            os.system("./run_flexdock.sh")
    if opt.job == 'translig':
        translig(opt.ligand)

@ -312,17 +367,27 @@ if opt.software == 'dftb':
        geom = 'in.gen'

    dftb(geom,opt.job,opt.activeatoms,opt.method,opt.parapath,opt.dispersion,opt.kpts,opt.hcorr)
-    with open('run.sh','w') as fout:
-        print("""#!/bin/bash
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=1
-#SBATCH --time=168:0:0
-export OMP_NUM_THREADS={}
-cd $PWD
-cp cmmd.in dftb_in.hsd
-$DFTB_COMMAND cmmd.in > cmmd.out""".format(opt.nproc),file=fout)
-    os.system('sbatch run.sh')
+    if opt.slurm == "true":
+        with open('run.sh','w') as fout:
+            print("""#!/bin/bash
+    #SBATCH --nodes=1
+    #SBATCH --ntasks=1
+    #SBATCH --cpus-per-task=1
+    #SBATCH --time=168:0:0
+    export OMP_NUM_THREADS={}
+    cd $PWD
+    cp cmmd.in dftb_in.hsd
+    $DFTB_COMMAND cmmd.in > cmmd.out""".format(opt.nproc),file=fout)
+        os.system('sbatch run.sh')
+    else:
+        with open('run.sh','w') as fout:
+            print("""#!/bin/bash
+    export OMP_NUM_THREADS={}
+    cd $PWD
+    cp cmmd.in dftb_in.hsd
+    $DFTB_COMMAND cmmd.in > cmmd.out""".format(opt.nproc),file=fout)
+        os.system("chmod +x run.sh")
+        os.system('./run.sh')


 if opt.software == 'qe':
@ -330,33 +395,47 @@ if opt.software == 'qe':

 # RUNNING SCRIPT
 if opt.software == 'orca':
-    with open('run.sh','w') as fout:
-        print("""#!/bin/bash
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task={}
-#SBATCH --time=168:0:0
-export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
-export PATH=/home/adit/opt/openmpi411/bin:$PATH
-export OMP_NUM_THREADS=1
-cd $PWD
-$ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe""".format(opt.nproc),file=fout)
-    os.system('sbatch run.sh')
-
+    if opt.slurm=="true":
+        with open('run.sh','w') as fout:
+            print("""#!/bin/bash
+    #SBATCH --nodes=1
+    #SBATCH --ntasks=1
+    #SBATCH --cpus-per-task={}
+    #SBATCH --time=168:0:0
+    export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
+    export PATH=/home/adit/opt/openmpi411/bin:$PATH
+    export OMP_NUM_THREADS=1
+    cd $PWD
+    $ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe""".format(opt.nproc),file=fout)
+        os.system('sbatch run.sh')
+    else:
+        with open('run.sh','w') as fout:
+            print("""#!/bin/bash
+    cd $PWD
+    $ORCA_COMMAND cmmd.in > cmmd.out --oversubscribe""",file=fout)
+        os.system("chmod +x run.sh")
+        os.system('./run.sh')
 if opt.software == 'nwchem':
-    with open('run.sh','w') as fout:
-        print("""#!/bin/bash
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task={}
-#SBATCH --time=168:0:0
-export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
-export PATH=/home/adit/opt/openmpi411/bin:$PATH
-export OMP_NUM_THREADS=1
-cd $PWD
-$NWCHEM_COMMAND cmmd.in > cmmd.out""".format(opt.nproc),file=fout)
-    os.system('sbatch run.sh')
-
+    if opt.slurm=="true":
+        with open('run.sh','w') as fout:
+            print("""#!/bin/bash
+    #SBATCH --nodes=1
+    #SBATCH --ntasks=1
+    #SBATCH --cpus-per-task={}
+    #SBATCH --time=168:0:0
+    export LD_LIBRARY_PATH=/home/adit/opt/openmpi411/lib:$LD_LIBRARY_PATH
+    export PATH=/home/adit/opt/openmpi411/bin:$PATH
+    export OMP_NUM_THREADS=1
+    cd $PWD
+    $NWCHEM_COMMAND cmmd.in > cmmd.out""".format(opt.nproc),file=fout)
+        os.system('sbatch run.sh')
+    else:
+        with open('run.sh','w') as fout:
+            print("""#!/bin/bash
+    cd $PWD
+    $NWCHEM_COMMAND cmmd.in > cmmd.out""",file=fout)
+        os.system("chmod +x run.sh")
+        os.system('./run.sh')
 if opt.software == 'qe':
    with open('run.sh','w') as fout:
        print("""#!/bin/bash
@ -403,4 +482,4 @@ 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,opt.solvent,opt.charge,opt.mult,opt.method,opt.fixedatoms,opt.fixedelements)
+    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,opt.charge,opt.mult,opt.method,opt.fixedatoms,opt.fixedelements,opt.slurm)
--- a/lib/pycache/cmmde_dcdftb.cpython-39.pyc
+++ b/lib/pycache/cmmde_dcdftb.cpython-39.pyc
--- a/lib/pycache/cmmde_dftb.cpython-39.pyc
+++ b/lib/pycache/cmmde_dftb.cpython-39.pyc
--- a/lib/pycache/cmmde_dock.cpython-39.pyc
+++ b/lib/pycache/cmmde_dock.cpython-39.pyc
--- a/lib/pycache/cmmde_hubbard.cpython-39.pyc
+++ b/lib/pycache/cmmde_hubbard.cpython-39.pyc
--- a/lib/pycache/cmmde_mass.cpython-39.pyc
+++ b/lib/pycache/cmmde_mass.cpython-39.pyc
--- a/lib/pycache/cmmde_mdpro.cpython-39.pyc
+++ b/lib/pycache/cmmde_mdpro.cpython-39.pyc
--- a/lib/pycache/cmmde_nw.cpython-39.pyc
+++ b/lib/pycache/cmmde_nw.cpython-39.pyc
--- a/lib/pycache/cmmde_orca.cpython-39.pyc
+++ b/lib/pycache/cmmde_orca.cpython-39.pyc
--- a/lib/pycache/cmmde_qe.cpython-39.pyc
+++ b/lib/pycache/cmmde_qe.cpython-39.pyc
--- a/lib/pycache/cmmde_xtb.cpython-39.pyc
+++ b/lib/pycache/cmmde_xtb.cpython-39.pyc
--- a/lib/cmmde_hubbard.py
+++ b/lib/cmmde_hubbard.py
@ -2,6 +2,7 @@ def azimuth(element):
    # Pemetaan bilangan kuantum azimut maksimum untuk masing-masing unsur    
    azimuth = {
    'Cl' : '3',
+    'Al' : '3',
    'H': '1',
    'Cu': '3',
    'O' : '2',
--- a/lib/cmmde_xtb.py
+++ b/lib/cmmde_xtb.py
@ -1,14 +1,18 @@
 # 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,solvent,charge,mult,method,fixedatoms,fixedelements):
+def xtb(job,geom,nproc,product,temperature,nrun,npoint,anopt,kpush,kpull,ppull,alp,distance,angle,dihedral,scanmode,maxiter,scan,solvent,charge,mult,method,fixedatoms,fixedelements,slurm):
 	with open('run.sh','w') as fout:
-		print("""#!/bin/bash
+		if slurm == "true":
+			print("""#!/bin/bash
 #SBATCH --nodes=1
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=1
 #SBATCH --time=168:0:0
 export OMP_NUM_THREADS={}
-cd $PWD""".format(nproc),file=fout)
+cd $PWD""".format(nproc), file=fout)
+		else:
+			print("""#!/bin/bash
+export OMP_NUM_THREADS={}""".format(nproc),file=fout)
 		meth = ''
 		if 'GFN-FF' in method or 'gfnff' in method:
 			meth += '--gfnff'
@ -108,9 +112,13 @@ $end""".format(nrun,npoint,anopt,kpush,kpull,ppull,alp),file=f)
 			print("""$opt
  maxcycle = {}""".format(maxiter),file=f)

-
-	os.system('sbatch run.sh')
+	if slurm == "true":
+		os.system('sbatch run.sh')
+	else:
+		os.system('chmod +x run.sh')
+		os.system('./run.sh')
 	

 	

+