#es_software = "gaussian"
istep = 0
fstep = 1 #3000
njobs = 1 #600
for njob in range(njobs):
job_init_step, job_final_step = step2_many_body.curr_and_final_step_job(
istep, fstep, njobs, njob)
nsteps_this_job = job_final_step - job_init_step + 1
print('\n1- We are before creating job ', njob, ' in directory:',
os.getcwd())
# Here we create the jobs through auxiliary_functions.cp2k_distribute
if es_software.lower() == "cp2k":
CP2K_methods.cp2k_distribute(job_init_step, job_final_step,
nsteps_this_job, trajectory_xyz_file,
es_software_input_template, njob)
elif es_software.lower() == "gaussian":
Gaussian_methods.gaussian_distribute(job_init_step, job_final_step,
nsteps_this_job,
trajectory_xyz_file,
es_software_input_template, njob)
print('2- Finished distributing for job ', njob,
'\nNow we are in directory', os.getcwd())
os.chdir("wd/job" + str(njob) + "/")
print('3- Now we have changed directory to :', os.getcwd(),
'To submit job', njob)
os.mkdir("cubefiles")
def run_step2_jobs(params):
""" Prepares and runs job folders needed for running step2
Args:
params (dict): The parameters dictionary used for containing
the variables needed to make the submit.slm template
Returns:
None: but creates the wd (working diretory) that stores the
job folders and the files needed to run each job, and runs
those jobs.
"""
logger.debug("Entered into the function initialize_step2_jobs")
critical_params = []
default_params = {
"trajectory_xyz_filename": "md.xyz",
"es_software": "cp2k",
"es_software_input_template": "cp2k_input_template",
"istep": 0,
"fstep": 1,
"njobs": 1,
"waveplot_input_template": "waveplot_in.hsd"
}
comn.check_input(params, default_params, critical_params)
logger.debug("Checked params in the function initialize_step2_jobs")
# Consider using shutils module here instead of os.system()
os.system("rm -r wd")
os.mkdir('wd')
os.system("rm -r res")
os.mkdir('res')
# Get the neededvariables from the params dictionary
trajectory_xyz_filename = params["trajectory_xyz_filename"]
es_software = params["es_software"]
es_software_input_template = params["es_software_input_template"]
init_md_step = params["istep"]
final_md_step = params["fstep"]
njobs = params["njobs"]
if es_software == "dftb+":
waveplot_input_template = params["waveplot_input_template"]
# Initialize the jobs
for njob in range(njobs):
logger.debug(f"Within the loops over njobs, initializing job: {njob}")
job_init_step, job_final_step = step2_many_body.curr_and_final_step_job(
init_md_step, final_md_step, njobs, njob)
nsteps_this_job = job_final_step - job_init_step + 1
logger.debug(
f"The initial step for the job {njob} is: {job_init_step} with final step: {job_final_step}"
)
logger.debug(f"nsteps_this_job is: {nsteps_this_job}")
logger.debug(f"Creating job: {njob} in directory: {os.getcwd()}")
if es_software.lower() == "cp2k":
logger.debug("es_software.lower() == cp2k")
CP2K_methods.cp2k_distribute(job_init_step, job_final_step,
nsteps_this_job,
trajectory_xyz_filename,
es_software_input_template, njob)
elif es_software.lower() == "gaussian":
logger.debug("es_software.lower() == gaussian")
Gaussian_methods.gaussian_distribute(job_init_step, job_final_step,
nsteps_this_job,
trajectory_xyz_filename,
es_software_input_template,
njob)
elif es_software.lower() == "dftb+":
logger.debug("es_software.lower() == dftb+")
DFTB_methods.dftb_distribute(job_init_step, job_final_step,
nsteps_this_job,
trajectory_xyz_filename,
es_software_input_template,
waveplot_input_template, njob)
logger.debug(
f"Finished distributing for job: {njob}. We are currently in directory: {os.getcwd()}"
)
os.chdir("wd/job" + str(njob) + "/")
logger.debug(f"Changed directory to: {os.getcwd()}")
logger.debug(
"Assigning values to the variables job_init_step, nsteps_this_job, and njob in submit_template.slm"
)
os.system("cp ../../submit_template.slm submit_" + str(njob) + ".slm")
# Now, open the submit_template file in this job folder
# Add the values to the params for this job
f = open("submit_" + str(njob) + ".slm")
submit_template_file = f.readlines()
submit_template_file_size = len(submit_template_file)
f.close()
f = open("submit_" + str(njob) + ".slm", 'w')
f.close()
for i in range(submit_template_file_size):
f = open("submit_" + str(njob) + ".slm", 'a')
submit_template_file_line = submit_template_file[i].split()
if not submit_template_file_line:
continue
elif submit_template_file_line[0] == "job_init_step=":
f.write("declare -i job_init_step=%i" % (job_init_step))
f.write("\n")
elif submit_template_file_line[0] == "nsteps_this_job=":
f.write("declare -i nsteps_this_job=%i" % (nsteps_this_job))
f.write("\n")
elif submit_template_file_line[0] == "njob=":
f.write("declare -i njob=%i" % (njob))
f.write("\n")
else:
f.write(submit_template_file[i])
logger.debug(f"Updated submit_template.slm")
os.system("sbatch submit_" + str(njob) + ".slm")
#os.system("sh submit_"+str(njob)+".slm")
logger.debug(f"Submitting the job in folder: {os.getcwd()}")
# Change directory back to the top directory
os.chdir("../../")
logger.debug(
f"Finished submitting job. We are now back in directory: {os.getcwd()}"
)