我正在尝试使用python代码创建并向gaussian提交多个作业运行此代码时:
for iframe in mols_xyz.trajectory:
mol_ind = iframe.frame + 1
g16_input = input_dir / f'{mol_base}_{mol_ind}.sh'
with g16_input.open('w') as fn:
fn.write('#!/bin/sh -l\n')
fn.write('\n')
fn.write('#$ -pe omp 8\n')
fn.write('#$ -P porcogrp\n')
fn.write('#$ -l h_rt=24:00:00\n')
fn.write('#$ -j y\n')
fn.write('\n')
fn.write('module load gaussian/16.A.03\n')
fn.write('\n')
fn.write(f'HOMEFOL={str(input_dir)}\n')
fn.write(f'INPUTFILE={str(input_dir)}/{mol_base}_{mol_ind}.com\n')
fn.write(f'OUTFILE={str(input_dir)}/{mol_base}_{mol_ind}.log\n')
fn.write('\n')
fn.write('SCRATCHDIR=/scratch/$USER/$JOB_ID\n')
fn.write('mkdir -p $SCRATCHDIR\n')
fn.write('cd $SCRATCHDIR\n')
fn.write('g16 $HOMEFOL/$INPUTFILE > $HOMEFOL/$OUTFILE')
os.system(qsub g16_input)
结果是:
[zpowers@scc1 Test]$ python gaussian_Input.py
File "gaussian_Input.py", line 59
os.system(qsub g16_input)
^
SyntaxError: invalid syntax
真的困在这里了,任何帮助都将不胜感激
您需要在系统调用周围加引号。该命令是一个字符串:
os.system('qsub g16_input')
见文件:https://docs.python.org/3.8/library/os.html#os.system
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