def setup(self, initdir): """ mv all files and directories (besides initdir) into initdir """ print("Moving files into initial run directory:", initdir) initdir = os.path.abspath(initdir) for my_prop in os.listdir(self.propdir): if (my_prop in io.VASP_INPUT_FILE_LIST + self.settings["extra_input_files"]) and (os.path.join( self.propdir, my_prop) != initdir): os.rename(os.path.join(self.propdir, my_prop), os.path.join(initdir, my_prop)) print("") sys.stdout.flush() # Keep a backup copy of the base INCAR shutil.copyfile(os.path.join(initdir, "INCAR"), os.path.join(self.propdir, "INCAR.base")) # If an initial incar is called for, copy it in and set the appropriate flag if (self.settings["initial"] != None) and (os.path.isfile( os.path.join(self.propdir, self.settings["initial"]))): new_values = io.Incar( os.path.join(self.propdir, self.settings["initial"])).tags io.set_incar_tag(new_values, initdir) print(" Set INCAR tags:", new_values, "\n") sys.stdout.flush()
def setup(self, initdir, settings): """ mv all files and directories (besides initdir) into initdir """ ### still has to handle the images print("Moving files and directories into initial run directory:", initdir) initdir = os.path.abspath(initdir) for p in os.listdir(self.calcdir): if (p in (io.VASP_INPUT_FILE_LIST + self.settings["extra_input_files"])) and (os.path.join( self.calcdir, p) != initdir): os.rename(os.path.join(self.calcdir, p), os.path.join(initdir, p)) ## copying the folders with image poscars into initdir for i in range(settings["n_images"] + 2): folder_name = str(i).zfill( 2) #max(2, len(str(settings["n_images"]))+1 )) ##too fancy!!! shutil.copytree(os.path.join(self.calcdir, "poscars", folder_name), os.path.join(initdir, folder_name)) print("") sys.stdout.flush() # Keep a backup copy of the base INCAR shutil.copyfile(os.path.join(initdir, "INCAR"), os.path.join(self.calcdir, "INCAR.base")) os.rename(os.path.join(initdir, "POSCAR"), os.path.join(self.calcdir, "POSCAR.start")) # If an initial incar is called for, copy it in and set the appropriate flag if (self.settings["initial"] != None) and (os.path.isfile( os.path.join(self.calcdir, self.settings["initial"]))): new_values = io.Incar( os.path.join(self.calcdir, self.settings["initial"])).tags io.set_incar_tag(new_values, initdir) print(" Set INCAR tags:", new_values, "\n") sys.stdout.flush()
def run(self): """ Perform a series of vasp jobs to relax a structure. Performs a series of vasp calculations until convergence is reached according to the criteria in 'status()'. Then performs a final constant volume run {"ISIF":2, "ISMEAR":-5, "NSW":0, "IBRION":-1}. """ print("Begin VASP convergence run") sys.stdout.flush() # get current status of the relaxation: (status, task) = self.status() print("\n++ status:", status, " next task:", task) sys.stdout.flush() while status == "incomplete": if task == "setup": self.add_rundir() self.setup(self.rundir[-1]) elif task == "relax": self.add_rundir() continue_job(self.rundir[-2], self.rundir[-1], self.settings) shutil.copyfile(os.path.join(self.propdir, "INCAR.base"), os.path.join(self.rundir[-1], "INCAR")) elif task == "constant": self.add_rundir() continue_job(self.rundir[-2], self.rundir[-1], self.settings) # set INCAR to ISIF = 2, ISMEAR = -5, NSW = 0, IBRION = -1 if (self.settings["final"] != None) and (os.path.isfile( os.path.join(self.propdir, self.settings["final"]))): new_values = io.Incar( os.path.join(self.propdir, self.settings["final"])).tags else: new_values = { "ISIF": 2, "ISMEAR": -5, "NSW": 0, "IBRION": -1 } # set INCAR system tag to denote 'final' if io.get_incar_tag("SYSTEM", self.rundir[-1]) is None: new_values["SYSTEM"] = "final" else: new_values["SYSTEM"] = io.get_incar_tag( "SYSTEM", self.rundir[-1]) + " final" io.set_incar_tag(new_values, self.rundir[-1]) print(" Set INCAR tags:", new_values, "\n") sys.stdout.flush() else: # probably hit walltime self.add_rundir() continue_job(self.rundir[-2], self.rundir[-1], self.settings) while True: # run vasp result = run(self.rundir[-1], npar=self.settings["npar"], ncore=self.settings["ncore"], command=self.settings["vasp_cmd"], ncpus=self.settings["ncpus"], kpar=self.settings["kpar"], err_types=self.settings["err_types"]) # if no errors, continue if result is None or self.not_converging(): # Check for actions that should be taken after the initial run if len(self.rundir) == 1: if self.settings["fine_ngx"]: outcarfile = os.path.join(self.rundir[-1], "OUTCAR") if not os.path.isfile(outcarfile): # This is an error but I'm not sure what to do about it pass else: init_outcar = io.Outcar(outcarfile) if not init_outcar.complete: # This is an error but I'm not sure what to do about it pass elif (init_outcar.ngx is None or init_outcar.ngy is None or init_outcar.ngz is None): # This is an error but I'm not sure what to do about it pass else: ng_tags = { "ngx": init_outcar.ngx * 2, "ngy": init_outcar.ngy * 2, "ngz": init_outcar.ngz * 2 } print(ng_tags) io.set_incar_tag(ng_tags, self.propdir, "INCAR.base") break # else, attempt to fix first error self.add_errdir() os.mkdir(self.rundir[-1]) # self.add_rundir() err = result.itervalues().next() print("\n++ status:", "error", " next task:", "fix_error") sys.stdout.flush() print("Attempting to fix error:", str(err)) err.fix(self.errdir[-1], self.rundir[-1], self.settings) print("") sys.stdout.flush() if (self.settings["backup"] != None) and len(self.rundir) > 1: print("Restoring from backups:") for my_file in self.settings["backup"]: if os.path.isfile( os.path.join(self.rundir[-2], my_file + "_BACKUP.gz")): f_in = gzip.open( os.path.join(self.rundir[-2], my_file + "_BACKUP.gz", 'rb')) f_out = open( os.path.join(self.rundir[-1], my_file, 'wb')) f_out.write(f_in.read()) f_in.close() f_out.close() print(my_file, " restored!") sys.stdout.flush() (status, task) = self.status() print("\n++ status:", status, " next task:", task) sys.stdout.flush() if status == "complete": if not os.path.isdir(self.finaldir): # mv final results to relax.final print("mv", os.path.basename(self.rundir[-1]), os.path.basename(self.finaldir)) sys.stdout.flush() os.rename(self.rundir[-1], self.finaldir) self.rundir.pop() complete_job(self.finaldir, self.settings) return (status, task)
def run(self): """ Perform a series of vasp jobs to run calculations. Performs a series of vasp calculations until convergence is reached according to the criteria in 'status()'. """ print("Begin VASP relaxation run") sys.stdout.flush() # get current status of the relaxation: (status, task) = self.status() print("\n++ status:", status, " next task:", task) sys.stdout.flush() while status == "incomplete": if task == "setup": self.add_rundir() self.setup(self.rundir[-1], self.settings) elif task == "new_run": self.add_rundir() # if "n_images" in settings then image CONTCARs will be copied casm.vasp.continue_job(self.rundir[-2], self.rundir[-1], self.settings) shutil.copyfile( os.path.join(self.calcdir, "INCAR.base"), os.path.join(self.rundir[-1], "INCAR")) ## should it be enforced?? elif task == "constant": self.add_rundir() # if "n_images" in settings then image CONTCARs will be copied casm.vasp.continue_job(self.rundir[-2], self.rundir[-1], self.settings) # set INCAR to ISIF = 2, ISMEAR = -5, NSW = 0, IBRION = -1 if (self.settings["final"] != None) and (os.path.isfile( os.path.join(self.calcdir, self.settings["final"]))): new_values = io.Incar( os.path.join(self.calcdir, self.settings["final"])).tags else: new_values = { "ISIF": 2, "ISMEAR": -5, "NSW": 0, "IBRION": -1 } # set INCAR system tag to denote 'final' if io.get_incar_tag("SYSTEM", self.rundir[-1]) is None: new_values["SYSTEM"] = "final" else: new_values["SYSTEM"] = io.get_incar_tag( "SYSTEM", self.rundir[-1]) + " final" io.set_incar_tag(new_values, self.rundir[-1]) print(" Set INCAR tags:", new_values, "\n") sys.stdout.flush() else: ## redundent self.add_rundir() casm.vasp.continue_job(self.rundir[-2], self.rundir[-1], self.settings) while True: # run vasp result = casm.vasp.run(self.rundir[-1], stdout="stdout", npar=self.settings["npar"], ncore=self.settings["ncore"], command=self.settings["vasp_cmd"], ncpus=self.settings["ncpus"], kpar=self.settings["kpar"], err_types=self.settings["err_types"], is_neb=True) # if no errors, continue if result is None or self.not_converging(): break # else, attempt to fix first error self.add_errdir() os.mkdir(self.rundir[-1]) # self.add_rundir() err = result.itervalues().next() print("\n++ status:", "error", " next task:", "fix_error") sys.stdout.flush() print("Attempting to fix error:", str(err)) err.fix(self.errdir[-1], self.rundir[-1], self.settings) print("") sys.stdout.flush() (status, task) = self.status() print("\n++ status:", status, " next task:", task) sys.stdout.flush() if status == "complete": if not os.path.isdir(self.finaldir): # mv final results to relax.final print("mv", os.path.basename(self.rundir[-1]), os.path.basename(self.finaldir)) sys.stdout.flush() os.rename(self.rundir[-1], self.finaldir) self.rundir.pop() casm.vasp.complete_job(self.finaldir, self.settings) return (status, task)