def _lammps_input_get_non_mast_keywords(self):
"""Get the non-LAMMPS keywords and make a dictionary."""
input_dict = dict()
allowedpath = os.path.join(dirutil.get_mast_install_path(), 'MAST',
'ingredients', 'programkeys',
'lammps_allowed_keywords.py')
allowed_list = self._lammps_input_get_allowed_keywords(allowedpath)
for key, value in self.keywords['program_keys'].iteritems():
if not key[0:5] == "mast_":
keytry = key.upper()
if not (keytry in allowed_list):
self.logger.warning(
"Ignoring program key %s for INPUT. To allow this keyword, add it to %s"
% (keytry, allowedpath))
else:
if type(value) == str and value.isalpha():
input_dict[keytry.lower()] = value
else:
input_dict[keytry.lower()] = value
if 'autocorrect' in input_dict:
input_dict['autocorrect'] = bool(input_dict['autocorrect'])
else:
input_dict['autocorrect'] = True
if input_dict['autocorrect']:
input_dict = readable_lammps_parameters(input_dict,
self.keywords['structure'])
return input_dict
def get_citations(recipedir):
"""Use mast_exec lines from the recipe directory in order
to assign a CITATIONS section to the SUMMARY.txt file.
Args:
recipedir <str>: Recipe directory
Returns:
linelist <list of str>: Lines to add to SUMMARY.txt
"""
mylist = list()
mylist = ['mast', 'pymatgen',
'spglib'] #need to use; removed python as standard
myinput = os.path.join(recipedir, "input.inp")
mastexecs = fileutil.grepme(myinput, "mast_exec")
for mastexec in mastexecs:
if 'vasp' in mastexec.lower():
mylist.append('vasp')
mastxcs = fileutil.grepme(myinput, "mast_xc")
if len(mastxcs) >= 1:
mylist.append('vasp_pps')
for mastxc in mastxcs:
if ("pw" in mastxc.lower()) or ("paw" in mastxc.lower()):
mylist.append('vasp_paw')
mastprogs = fileutil.grepme(myinput, "mast_program")
if len(mastprogs) >= 1:
for mastprog in mastprogs:
if ("vasp_neb" in mastprog.lower()):
mylist.append('vaspneb')
if "tst" in mastexec.lower():
mylist.append('vaspneb')
#if 'phon' in mastexec.lower():
# mylist.append('phon')
if 'structopt' in mastexec.lower():
mylist.append('structopt')
mastwrites = fileutil.grepme(myinput, "mast_write_method")
for mastwrite in mastwrites:
if 'pathfinder' in mastexec.lower():
mylist.append('pathfinder')
citationpath = os.path.join(dirutil.get_mast_install_path(), "summary",
"citation_files")
citationfiles = os.listdir(citationpath)
linelist = list()
uniquelist = list()
for mylistitem in mylist:
if not mylistitem in uniquelist:
uniquelist.append(mylistitem)
#print "UNIQUELIST: ", uniquelist
for listitem in uniquelist:
for citationfile in citationfiles:
if citationfile[:-3] == listitem: #all except number
cfpath = os.path.join(citationpath, citationfile)
cffile = MASTFile(cfpath)
linelist.extend(cffile.data)
return linelist
def get_citations(recipedir):
"""Use mast_exec lines from the recipe directory in order
to assign a CITATIONS section to the SUMMARY.txt file.
Args:
recipedir <str>: Recipe directory
Returns:
linelist <list of str>: Lines to add to SUMMARY.txt
"""
mylist=list()
mylist=['mast','pymatgen','spglib'] #need to use; removed python as standard
myinput = os.path.join(recipedir, "input.inp")
mastexecs = fileutil.grepme(myinput, "mast_exec")
for mastexec in mastexecs:
if 'vasp' in mastexec.lower():
mylist.append('vasp')
mastxcs = fileutil.grepme(myinput, "mast_xc")
if len(mastxcs) >= 1:
mylist.append('vasp_pps')
for mastxc in mastxcs:
if ("pw" in mastxc.lower()) or ("paw" in mastxc.lower()):
mylist.append('vasp_paw')
mastprogs = fileutil.grepme(myinput, "mast_program")
if len(mastprogs) >= 1:
for mastprog in mastprogs:
if ("vasp_neb" in mastprog.lower()):
mylist.append('vaspneb')
if "tst" in mastexec.lower():
mylist.append('vaspneb')
#if 'phon' in mastexec.lower():
# mylist.append('phon')
if 'structopt' in mastexec.lower():
mylist.append('structopt')
mastwrites = fileutil.grepme(myinput, "mast_write_method")
for mastwrite in mastwrites:
if 'pathfinder' in mastexec.lower():
mylist.append('pathfinder')
citationpath = os.path.join(dirutil.get_mast_install_path(),
"summary","citation_files")
citationfiles = os.listdir(citationpath)
linelist = list()
uniquelist=list()
for mylistitem in mylist:
if not mylistitem in uniquelist:
uniquelist.append(mylistitem)
#print "UNIQUELIST: ", uniquelist
for listitem in uniquelist:
for citationfile in citationfiles:
if citationfile[:-3] == listitem: #all except number
cfpath = os.path.join(citationpath, citationfile)
cffile = MASTFile(cfpath)
linelist.extend(cffile.data)
return linelist
def _phon_inphon_get_non_mast_keywords(self):
"""Sort out the non-PHON keywords and make a dictionary."""
inphon_dict=dict()
allowedpath = os.path.join(dirutil.get_mast_install_path(),
'ingredients','programkeys','phon_allowed_keywords.py')
allowed_list = self._phon_inphon_get_allowed_keywords(allowedpath)
for key, value in self.keywords['program_keys'].iteritems():
if not key[0:5] == "mast_":
keytry = key.upper()
if not (keytry in allowed_list):
self.logger.warning("Ignoring program key %s for INPHON. To allow this keyword, add it to %s" % (keytry, allowedpath))
else:
if type(value)==str and value.isalpha():
inphon_dict[keytry]=value.capitalize() #First letter cap
else:
inphon_dict[keytry]=value
return inphon_dict
def _lammps_input_get_non_mast_keywords(self):
"""Get the non-LAMMPS keywords and make a dictionary."""
input_dict=dict()
allowedpath = os.path.join(dirutil.get_mast_install_path(),
'ingredients','programkeys','lammps_allowed_keywords.py')
allowed_list = self._lammps_input_get_allowed_keywords(allowedpath)
for key, value in self.keywords['program_keys'].iteritems():
if not key[0:5] == "mast_":
keytry = key.upper()
if not (keytry in allowed_list):
self.logger.warning("Ignoring program key %s for INPUT. To allow this keyword, add it to %s" % (keytry, allowedpath))
else:
if type(value)==str and value.isalpha():
input_dict[keytry.lower()]=value
else:
input_dict[keytry.lower()]=value
return input_dict
def _phon_inphon_get_non_mast_keywords(self):
"""Sort out the non-PHON keywords and make a dictionary."""
inphon_dict = dict()
allowedpath = os.path.join(dirutil.get_mast_install_path(),
'ingredients', 'programkeys',
'phon_allowed_keywords.py')
allowed_list = self._phon_inphon_get_allowed_keywords(allowedpath)
for key, value in self.keywords['program_keys'].iteritems():
if not key[0:5] == "mast_":
keytry = key.upper()
if not (keytry in allowed_list):
self.logger.warning(
"Ignoring program key %s for INPHON. To allow this keyword, add it to %s"
% (keytry, allowedpath))
else:
if type(value) == str and value.isalpha():
inphon_dict[keytry] = value.capitalize(
) #First letter cap
else:
inphon_dict[keytry] = value
return inphon_dict
import MAST
from MAST.ingredients.pmgextend.structure_extensions import StructureExtensions
import shutil
import pymatgen
import numpy as np
from MAST.utility import dirutil
testname = "fss_structure_test"
#oldcontrol = os.getenv("MAST_CONTROL")
#oldrecipe = os.getenv("MAST_RECIPE_PATH")
#oldscratch = os.getenv("MAST_SCRATCH")
#print "Old directories:"
#print oldcontrol
#print oldrecipe
#print oldscratch
testdir = os.path.join(dirutil.get_mast_install_path(), 'test', testname)
class TestSE(unittest.TestCase):
"""Test StructureExtensions
"""
def setUp(self):
os.chdir(testdir)
def tearDown(self):
pass
def test_scale_structure(self):
size = '1 1 0,-1 1 0,0 0 1'
perfect = pymatgen.io.vaspio.Poscar.from_file(
"POSCAR_perfect").structure
"""Tests for Recipe for FSS"""
import unittest
from unittest import SkipTest
import os
import time
import MAST
import pymatgen
from MAST.utility import dirutil
from MAST.recipe import recipeutility
from MAST.utility import MASTFile
testname = "fss_recipe_test"
testdir = os.path.join(dirutil.get_mast_install_path(), "test", testname)
class TestRecipeUtility(unittest.TestCase):
def setUp(self):
os.chdir(testdir)
def tearDown(self):
pass
def test_read_recipe(self):
fss_recipe = MASTFile(os.path.join(testdir, "fss_recipe.txt"))
fss_recipe_lines = fss_recipe.data
fss_recipe_lines.pop(0) # remove recipe name
[htu, ptc, htr] = recipeutility.read_recipe(fss_recipe_lines)
self.assertEqual(htu["defect_2x2x3_int1_opt"]["neb_2x2x3_int1-int2_opt"], "relax_to_neb")
self.assertItemsEqual(ptc["neb_1x2x4_int1-int2_opt"], ["defect_1x2x4_int1_opt", "defect_1x2x4_int2_opt"])
self.assertEqual(htr["phonon_1x1x2_int1-int2_w0"], "phonon")
# Maintainer: Tam Mayeshiba
# Last updated: 2014-04-25
##############################################################
# Purpose: Modify and get information out of submission scripts.
# 11/9/12 created
import os
import sys
import math #TA to calc num_nodes
import importlib
from MAST.utility.mastfile import MASTFile
from MAST.utility import MASTError
from MAST.utility import dirutil
mast_control = dirutil.get_mast_control_path()
mast_install = dirutil.get_mast_install_path()
mast_platform = dirutil.get_mast_platform()
#mysc = "submit.platforms.script_commands_%s" % mast_platform
#my_script_commands = importlib.import_module(mysc)
"""
Script commands
"""
def write_submit_script(keywords):
"""This script example is built on the following ingredient keywords,
and may require significant customization.
mast_processors
mast_ppn
mast_queue
# Maintainer: Tam Mayeshiba
# Last updated: 2014-04-25
##############################################################
# Purpose: Modify and get information out of submission scripts.
# 11/9/12 created
import os
import sys
import math #TA to calc num_nodes
import importlib
from MAST.utility.mastfile import MASTFile
from MAST.utility import MASTError
from MAST.utility import dirutil
mast_control = dirutil.get_mast_control_path()
mast_install = dirutil.get_mast_install_path()
mast_platform = dirutil.get_mast_platform()
#mysc = "submit.platforms.script_commands_%s" % mast_platform
#my_script_commands = importlib.import_module(mysc)
"""
Script commands
"""
def write_submit_script(keywords):
"""This script example is built on the following ingredient keywords,
and may require significant customization.
mast_processors