diff --git a/bin/cmmde.py b/bin/cmmde.py index 91b7adc..817ebd4 100755 --- a/bin/cmmde.py +++ b/bin/cmmde.py @@ -487,14 +487,14 @@ if opt.software == 'gromacs': #SBATCH --time=168:0:0 export OMP_NUM_THREADS=1 cd $PWD -$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {} -nnpt {} -comp {} -np {}""".format(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,opt.nproc,opt.rcol),file=fout) +$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {} -nnpt {} -comp {} -np {} -rc {} -t {}""".format(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,opt.nproc,opt.rcol,opt.temp),file=fout) os.system('sbatch run.sh') else: with open('run.sh','w') as fout: print("""#!/bin/bash export OMP_NUM_THREADS=1 cd $PWD -$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {} -nnpt {} -comp {} -np {}""".format(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,opt.nproc,opt.rcol),file=fout) +$GROMACS_COMMAND -mt {} -mp {} -ct {} -pt {} -pp {} -l {} -cat {} -gen {} -Nump {} -prod {} -nprod {} -nequil {} -dt {} -ctype {} -nnpt {} -comp {} -np {} -rc {} -t {}""".format(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,opt.nproc,opt.rcol,opt.temp),file=fout) os.system('chmod +x run.sh') os.system('./run.sh') diff --git a/lib/__pycache__/cmmde_rdf.cpython-310.pyc b/lib/__pycache__/cmmde_rdf.cpython-310.pyc index d20cad8..b3a01cf 100644 Binary files a/lib/__pycache__/cmmde_rdf.cpython-310.pyc and b/lib/__pycache__/cmmde_rdf.cpython-310.pyc differ diff --git a/lib/cmmde_rdf.py b/lib/cmmde_rdf.py index 50c7804..372e9de 100644 --- a/lib/cmmde_rdf.py +++ b/lib/cmmde_rdf.py @@ -15,8 +15,9 @@ def rdf(traject,latt,pair,endrange,resolution): cell.append(list(map(float, line.split()[1:4]))) box = lattice.Lattice(cell) - (lx, ly, lz), (a, b, c) = box.lengths_and_angles - + # (lx, ly, lz), (a, b, c) = box.lengths_and_angles + lx, ly, lz = box.lengths + a, b, c = box.angles u = MDAnalysis.Universe(traject, format='XYZ') u.dimensions = np.array([lx, ly, lz, a, b, c], dtype=np.float32)