diff --git a/bin/cmmde.py b/bin/cmmde.py index 4eb17b2..2d059b8 100755 --- a/bin/cmmde.py +++ b/bin/cmmde.py @@ -449,19 +449,32 @@ mpirun -np {} $QE_COMMAND < cmmd.in > cmmd.out""".format(opt.nproc,opt.nproc),fi os.system('sbatch run.sh') if opt.software == 'dcdftb': - os.system("cp cmmd.in dftb.inp") - 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={} + if opt.slurm == 'true': + os.system("cp cmmd.in dftb.inp") + 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 + $DCDFTB_COMMAND + mv dftb.out cmmd.out + mv traject traject.xyz""".format(opt.nproc),file=fout) + os.system('sbatch run.sh') + else: + os.system("cp cmmd.in dftb.inp") + with open('run.sh','w') as fout: + print("""#!/bin/bash cd $PWD $DCDFTB_COMMAND mv dftb.out cmmd.out -mv traject traject.xyz""".format(opt.nproc),file=fout) - os.system('sbatch run.sh') +if [-f traject.xyz]; then +mv traject traject.xyz +fi""",file=fout) + os.system("chmod +x run.sh") + os.system('./run.sh') if opt.software == 'gromacs': if opt.slurm == 'true': diff --git a/lib/__pycache__/cmmde_msd_com.cpython-310.pyc b/lib/__pycache__/cmmde_msd_com.cpython-310.pyc new file mode 100644 index 0000000..e7b905e Binary files /dev/null and b/lib/__pycache__/cmmde_msd_com.cpython-310.pyc differ diff --git a/lib/__pycache__/cmmde_rdf.cpython-310.pyc b/lib/__pycache__/cmmde_rdf.cpython-310.pyc new file mode 100644 index 0000000..d20cad8 Binary files /dev/null and b/lib/__pycache__/cmmde_rdf.cpython-310.pyc differ