From ead8c97047fc8b9c130c4d2c6ca9074b483df474 Mon Sep 17 00:00:00 2001
From: Thomas Young Cluster RITS Do NOT reset password
<mmm0586@login04.thomas.ucl.ac.uk>
Date: Mon, 21 Oct 2019 22:03:42 +0100
Subject: [PATCH 1/5] Revise incar.py with two new classes *Param* and
*Params*, still compatible with previous usage, and make INCAR writing simple
and extendable with VASP INCAR Parameters DataBase (vasp_para_db.py).
---
vaspy/incar.py | 567 +++++++++++++++++++++++++++++++-----------
vaspy/vasp_para_db.py | 173 +++++++++++++
2 files changed, 597 insertions(+), 143 deletions(-)
create mode 100644 vaspy/vasp_para_db.py
diff --git a/vaspy/incar.py b/vaspy/incar.py
index 18b65ae..64a3fa4 100644
--- a/vaspy/incar.py
+++ b/vaspy/incar.py
@@ -5,191 +5,210 @@
========================================================================
Written by PytLab <shaozhengjiang@gmail.com>, October 2015
Updated by PytLab <shaozhengjiang@gmail.com>, July 2016
+Revised by jyxu <jxu15@qub.ac.uk>, October 2019
========================================================================
"""
+import os
+import sys
+
import logging
+import warnings
from vaspy import VasPy
+from vaspy.vasp_para_db import *
-class InCar(VasPy):
- def __init__(self, filename='INCAR'):
+class Param(VasPy):
+ def __init__(self, pname, pvalue='', pcomm=''):
"""
- Create a INCAR file class.
+ Create a INCAR parameter class.
Example:
-
- >>> a = InCar()
+ >>> para = Param('SYSTEM')
Class attributes descriptions
=======================================================
Attribute Description
============ =======================================
- filename string, name of INCAR file
+ pname string, parameter name
+ pvalue string/int/flaot, parameter value
+ pcomm string, parameter comment
============ =======================================
+
"""
- super(self.__class__, self).__init__(filename)
- self.filename = filename
- self.load()
+ __slots__ = ('para', 'pname', 'pvalue', 'pcomm')
- # Set logger.
- self.__logger = logging.getLogger("vaspy.InCar")
+ self._pname, self._pvalue, self._pcomm = None, None, None
- def load(self):
- "Load all data in INCAR."
- tot_pnames, tot_datas = [], []
- with open(self.filename, 'r') as f:
- for line in f:
- matched = self.rdata(line)
- if matched:
- pnames, datas = matched
- tot_pnames.extend(pnames)
- tot_datas.extend(datas)
- # set attrs
- for pname, data in zip(tot_pnames, tot_datas):
- setattr(self, pname, data)
-
- # Set parameter names and data lists.
-# sorted_pnames, sorted_datas = self.__sort_two_lists(tot_pnames, tot_datas)
-# self.pnames = sorted_pnames
-# self.datas = sorted_datas
- self.pnames = tot_pnames
- self.datas = tot_datas
+ self.pname = pname
+ self.pvalue, self.pcomm = str(pvalue), str(pcomm)
- return
+ self.__logger = logging.getLogger("vaspy.Param")
- def __sort_two_lists(self, list1, list2):
- """
- Private helper function to sort two lists.
- """
- assert len(list1) == len(list2)
- # Sort the pairs according the entries of list1.
- sorted_pairs = sorted(zip(list1, list2), key=lambda pair: pair[0])
- sorted_list1, sorted_list2 = [list(x) for x in zip(*sorted_pairs)]
+ @property
+ def pname(self):
+ """Parameter Name"""
+ return self._pname
- return sorted_list1, sorted_list2
+ @pname.setter
+ def pname(self, name):
+ """"""
+ name = name.upper()
+ if name not in INCAR_PARAMETERS.keys():
+ raise ValueError("Unknown Parameter <%s> in VASP INCAR Database." %name)
+ self._pname = name
- @staticmethod
- def rdata(line):
- "Get INCAR data(s) in a line."
- line = line.strip()
- if not line or line.startswith(('!', '#')):
- return None
+ return
+
+ @property
+ def pvalue(self):
+ """Parameter Value"""
+ return self._pvalue
+
+ @pvalue.setter
+ def pvalue(self, value):
+ """"""
+ optional_values = [str(v) for v in INCAR_PARAMETERS[self.pname][1]]
+
+ # check optional values, under development
+ '''
+ if optional_values == [] or value in optional_values:
+ pass
else:
- if '#' in line:
- line = line.split('#')[0].strip()
- if '!' in line:
- line = line.split('!')[0].strip()
- elif '!' in line:
- line = line.split('!')[0].strip()
- # get parameter name and data
- if ';' in line:
- params = [param.strip() for param in line.split(';')]
- else:
- params = [line]
- pnames, datas = [], []
- for param in params:
- pname, data = [i.strip() for i in param.split('=')]
- pnames.append(pname)
- datas.append(data)
+ raise ValueError("Unknown Value <%s> for Parameter <%s>." \
+ %(value, self.pname))
+ '''
+
+ if value != '':
+ default_value = value
+ else:
+ default_value = INCAR_PARAMETERS[self.pname][0]
- return pnames, datas
+ self._pvalue = str(default_value)
- def set(self, pname, data):
- """
- Set a named parameter of InCar object.
+ return
- Example:
- --------
- >>> incar_obj.set("ISIF", 2)
- """
- if not hasattr(self, pname):
- raise ValueError('%s is not in INCAR, ' +
- 'Use add() instead.' % pname)
- setattr(self, pname, str(data))
+ @property
+ def pcomm(self):
+ """Parameter Comment"""
+ return self._pcomm
- return
+ @pcomm.setter
+ def pcomm(self, comm):
+ """"""
+ if comm == '':
+ comm = " ".join((COMMSIGN, INCAR_PARAMETERS[self.pname][2]))
+ else:
+ if not comm.startswith(COMMSIGN):
+ comm = " ".join((COMMSIGN, comm))
- def add(self, pname, data):
- """
- Add a new parameter name to InCar object.
+ self._pcomm = comm
- Example:
- --------
- >>> incar_obj.add("ISIF", 2)
+ return
+
+ @property
+ def para(self):
+ """"""
+ return (self.pname, self.pvalue, self.pcomm)
+
+ def __add__(self, another):
+ """
+ Overload the add operator, a *Param* adds a *Param*/*Params* equal *Params*.
"""
- data = str(data)
- if hasattr(self, pname):
- msg = "{} is already in INCAR, set to {}".format(pname, data)
- self.__logger.warning(msg)
+ if isinstance(another, Param):
+ return Params((self, another))
+ elif isinstance(another, Params):
+ return Params((self,) + another.paras)
else:
- self.pnames.append(pname)
- setattr(self, pname, data)
+ raise ValueError("Add must also be a *Param*/*Params* object.")
- return
+ def __repr__(self):
+ return str(self.para)
- def pop(self, pname):
+
+class Params(VasPy):
+ def __init__(self, paras=()):
"""
- Delete a parameter from InCar object.
+ Create a INCAR parameters class.
+ """
+ # set logger
+ self.__logger = logging.getLogger("vaspy.Params")
- Returns:
- --------
- parameter name, parameter value.
+ if paras == ():
+ self.paras = ()
+ elif isinstance(paras, list) or isinstance(paras, tuple):
+ self.paras = self.remove_duplicates(paras)
+ else:
+ self("%s must be a *list* or *tuple* object." %paras)
+
+ def remove_duplicates(self, paras):
+ """Remove duplicates in paras, return a tuple"""
+ paras_list = []
+ for para in paras:
+ if isinstance(para, Param):
+ pnames = [p.pname for p in paras_list]
+ if para.pname in pnames:
+ warnings.warn("Duplicate parameter " + \
+ "%s, value %s(old) %s(new), the new one is not read."\
+ %(para.pname, paras_list[pnames.index(para.pname)], \
+ para.pvalue), RuntimeWarning)
+ else:
+ paras_list.append(para)
+ else:
+ raise ValueError("%s must be a *Param* object." %para)
- Example:
- --------
- >>> incar_obj.del("ISIF")
- """
- if not hasattr(self, pname):
- msg = "InCar has no parameter '{}'".format(pname)
- self.__logger.warning(msg)
- return
+ return tuple(paras_list)
+
+ @property
+ def pnames(self):
+ """Return all parameters' names."""
+ self._pnames = [p.pname for p in self.paras]
- # Delete from pnames and datas.
- idx = self.pnames.index(pname)
- self.pnames.pop(idx)
- data = self.datas.pop(idx)
+ return tuple(self._pnames)
- # Delete attribute.
- del self.__dict__[pname]
+ @property
+ def pvalues(self):
+ """"""
+ self._pvalues = [p.pvalue for p in self.paras]
- return pname, data
+ return tuple(self._pvalues)
- def compare(self, another):
- """
- Function to compare two InCar objects.
-
- Parameters:
- -----------
- another: Another InCar object.
+ def get_para(self, name):
+ """"""
+ return self.paras[self.pnames.index(name)]
- Returns:
- --------
- A tuple of two dictionaries containing difference informations.
+ def get_pvalue(self, name):
+ """"""
+ return self.pvalues[self.pnames.index(name)]
+
+ def __compare(self, another):
"""
- tot_pnames = set(self.pnames + another.pnames)
+ Private method to compare two Params object.
+ """
+ self_pnames, another_pnames = self.pnames, another.pnames
+ tot_pnames = set(list(self_pnames) + list(another_pnames))
self_dict, another_dict = {}, {}
for pname in tot_pnames:
# If both have, check the difference.
- if (pname in self.pnames and pname in another.pnames):
- self_data = getattr(self, pname)
- another_data = getattr(another, pname)
- if self_data != another_data:
- self_dict.setdefault(pname, self_data)
- another_dict.setdefault(pname, another_data)
+ if (pname in self_pnames and pname in another_pnames):
+ self_pvalue = self.get_pvalue(pname)
+ another_pvalue = self.get_pvalue(pname)
+ if self_pvalue != another_pvalue:
+ self_dict.setdefault(pname, self_pvalue)
+ another_dict.setdefault(pname, another_pvalue)
else:
# Only in this object.
- if pname in self.pnames:
- self_data = getattr(self, pname)
- self_dict.setdefault(pname, self_data)
+ if pname in self_pnames:
+ self_pvalue = self.get_pvalue(pname)
+ self_dict.setdefault(pname, self_pvalue)
another_dict.setdefault(pname, "")
# Only in the other object.
else:
- another_data = getattr(another, pname)
- another_dict.setdefault(pname, another_data)
+ another_pvalue = self.get_pvalue(pname)
+ another_dict.setdefault(pname, another_pvalue)
self_dict.setdefault(pname, "")
return self_dict, another_dict
@@ -198,7 +217,8 @@ def __eq__(self, another):
"""
Overload euqal operator function.
"""
- self_dict, another_dict = self.compare(another)
+ self_dict, another_dict = self.__compare(another)
+ # print(self_dict, another_dict)
if (not self_dict) and (not another_dict):
return True
@@ -214,20 +234,281 @@ def __ne__(self, another):
else:
return True
- def tofile(self, filename=None):
- "Create INCAR file."
+ def __add__(self, another):
+ """
+ Overload add operator, append a *Param*/*Params* to a *Params*
+ """
+ if isinstance(another, Param):
+ paras = self.paras + (another,)
+ elif isinstance(another, Params):
+ paras = self.paras + another.paras
+
+ paras = self.remove_duplicates(paras)
+
+ return Params(paras)
+
+ def add(self, pname, pvalue=''):
+ """
+ Add a new parameter to *Params* object.
+ Now only param object are supported.
+ Different from __add__, which does not change the *Param* object.
+
+ Example:
+ --------
+ >>> paras.add('ISIF', 2)
+ """
+ para = Param(pname, pvalue)
+ paras = (self + para).paras
+ self.paras = paras
+
+ return self
+
+ def __sub__(self, another):
+ """
+ Overload sub operator, remove a *Param*/*Params* to a *Params*
+ """
+ if isinstance(another, Param):
+ paras = (para for para in self.paras if para.pname != another.pname)
+ elif isinstance(another, Params):
+ paras = (para for para in self.paras if para.pname not in another.pnames)
+
+ self.paras = tuple(paras)
+
+ return self
+
+ def set(self, name, value):
+ """
+ Set a named parameter of InCar object.
+
+ Example:
+ --------
+ >>> incar_obj.set("ISIF", 2)
+ """
+ if name not in self.pnames:
+ raise ValueError('%s is not in INCAR, ' + 'Use add() instead.' % name)
+
+ self.get_para(name).pvalue = str(value)
+
+ return
+
+ def pop(self, pname):
+ """
+ Delete a parameter from InCar object.
+
+ Returns:
+ --------
+ parameter name, parameter value.
+
+ Example:
+ --------
+ >>> incar_obj.pop("ISIF")
+ """
+ if pname not in self.pnames:
+ raise ValueError('%s is not in INCAR, ' + 'Use add() instead.' % name)
+
+ # Delete from pnames and datas.
+ value = self.get_pvalue(pname)
+ paras = (self - self.get_para(pname)).paras
+ self.paras = paras
+
+ return pname, value
+
+ def __len__(self):
+ """
+ Overload len operator, return the number of parameters.
+ """
+ return len(self.paras)
+
+ def __repr__(self):
+ """
+ """
+ return str(self.paras)
+
+
+class InCar(Params):
+ def __init__(self, src=None):
+ """
+ Create a INCAR file class.
+
+ Example:
+
+ >>> a = InCar()
+
+ Class attributes descriptions
+ =======================================================
+ Attribute Description
+ ============ =======================================
+ src string/Params, incar parameter source
+ ============ =======================================
+ """
+ # super(self.__class__, self).__init__(src)
+ if src is None:
+ self.paras = ()
+ else:
+ if isinstance(src, str):
+ if os.path.isfile(src):
+ self.filename = src
+ self.paras = self.load()
+ elif isinstance(src, Params):
+ self.paras = src.paras
+
+ self.paras = self.remove_duplicates(self.paras)
+ self.parasets = None
+
+ # set logger
+ self.__logger = logging.getLogger("vaspy.InCar")
+
+ def load(self):
+ "Load all data in INCAR."
+ tot_pnames, tot_pvalues, tot_pcomms = [], [], []
+ with open(self.filename, 'r') as reader:
+ for line in reader:
+ matched = self.rdata(line)
+ if matched:
+ pnames, pvalues, pcomms = matched
+ tot_pnames.extend(pnames)
+ tot_pvalues.extend(pvalues)
+ tot_pcomms.extend(pcomms)
+
+ paras_list = []
+ for pname, pvalue, pcomm in zip(tot_pnames, tot_pvalues, tot_pcomms):
+ para = Param(pname, pvalue, pcomm)
+ paras_list.append(para)
+
+ return tuple(paras_list)
+
+ @staticmethod
+ def rdata(line):
+ "Get INCAR data(s) in a line."
+ line = line.strip()
+ if not line or line.startswith(('!', '#')):
+ return None
+ else:
+ pnames, pvalues, pcomms = [], [], []
+ value, comm = '', ''
+ if '#' in line:
+ splitted_line = line.split('#')
+ value = splitted_line[0].strip()
+ comm = splitted_line[1].strip()
+ if '!' in value:
+ splitted_value = value.split('!')
+ value = splitted_value[0].strip()
+ comm = ' '.join(comm, splitted_value[1].strip())
+ elif '!' in line:
+ splitted_line = line.split('!')
+ value = splitted_line[0].strip()
+ comm = splitted_line[1].strip()
+ if '#' in value:
+ splitted_value = value.split('#')
+ value = splitted_value[0].strip()
+ comm = ' '.join(comm, splitted_value[1].strip())
+ else:
+ value = line
+ pcomms.append(comm)
+ # get parameter name and data
+ if ';' in value:
+ params = [param.strip() for param in value.split(';')]
+ else:
+ params = [value]
+ for param in params:
+ pname, pvalue = [i.strip() for i in param.split('=')]
+ pnames.append(pname)
+ pvalues.append(pvalue)
+
+ return pnames, pvalues, pcomms
+
+ def quickgen(self, tasks, **kargs):
+ """Quick generation of INCAR with built-in parameters."""
+ # check task
+ tasks = tasks.strip().split('-')
+ task_basic = ['SC']
+ if 'SC' not in tasks:
+ task_basic.extend(tasks)
+ tasks = task_basic
+
+ parasets = []
+ for task in tasks:
+ if task in BUILTIN_PARASETS.keys():
+ parasets.extend(BUILTIN_PARASETS[task][0])
+ else:
+ msg = "Unsupported INCAR parameter set %s." %task
+ self.__logger.error(msg)
+ sys.exit(1)
+
+ self.parasets = parasets
+
+ # load parasets
+ self.incar_categories = INCAR_PARACATEGORIES
+ pnames = []
+ for pset in self.parasets:
+ pnames.extend(list(self.incar_categories[pset]))
+
+ paras_list = []
+ for pname in pnames:
+ paras_list.append(Param(pname))
+
+ self.paras = tuple(paras_list)
+
+ # special settings for some task
+ paras_list = []
+ for task in tasks:
+ for para in BUILTIN_PARASETS[task][1]:
+ self.get_para(para[0]).pvalue = para[1]
+
+ # add more parameters along with built-in parasets
+ for key, value in kargs.items():
+ self.set(key, str(value))
+
+ return
+
+ def tostr(self):
+ """"""
content = '# Created by VASPy\n'
- for pname in self.pnames:
- if not hasattr(self, pname):
- raise ValueError('Unknown parameter: %s' % pname)
- data = str(getattr(self, pname))
- content += '%s = %s\n' % (pname, data)
+ if self.parasets:
+ tot_pnames = []
+ for pset in self.parasets:
+ content += '# %s\n' %pset
+ pnames = INCAR_PARACATEGORIES[pset]
+ tot_pnames.extend(pnames)
+ for pname in pnames:
+ para = self.get_para(pname)
+ content += PARAFORMAT.format(para.pname, para.pvalue, para.pcomm)
+ content += '\n'
+
+ other_pnames = [pname for pname in self.pnames \
+ if pname not in tot_pnames]
+ if len(other_pnames) != 0:
+ content += '# Additional\n'
+ for pname in other_pnames:
+ para = self.get_para(pname)
+ content += PARAFORMAT.format(para.pname, para.pvalue, para.pcomm)
+ content += '\n'
+ else:
+ for para in self.paras:
+ content += PARAFORMAT.format(para.pname, para.pvalue, para.pcomm)
- # Write to file.
+ return content
+
+ def tofile(self, filename='INCAR', verbos=True):
+ "Create INCAR file."
if filename is None:
- filename = self.filename
- with open(filename, 'w') as f:
- f.write(content)
+ self.__logger.error("Filename to write INCAR is needed.")
+ else:
+ if os.path.exists(filename):
+ self.__logger.warning("%s exists will be overrided." %filename)
+
+ content = self.tostr()
+ with open(filename, 'w') as writer:
+ writer.write(content)
+
+ self.__logger.info("Succesfully write incar obejct to %s." %filename)
+
+ if verbos:
+ print(content)
return
+
+ def __repr__(self):
+ """"""
+ return self.tostr()
diff --git a/vaspy/vasp_para_db.py b/vaspy/vasp_para_db.py
new file mode 100644
index 0000000..0afb121
--- /dev/null
+++ b/vaspy/vasp_para_db.py
@@ -0,0 +1,173 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Golabel Variables Descriptions (Most Frequently Used INCAR Parameters)
+===============================================================================
+ Attribute Description
+ ====================== ===================================================
+ COMMSIGN comment sign in INCAR file
+ PARAFORMAT format of parameter in INCAR
+ INCAR_PARAMETERS a dictionary of INCAR parameters
+ INCAR_PARACATEGORIES different groups of INCAR parameters
+ BUILTIN_PARASETS built-in parameter groups for quick-generation
+ ====================== ===================================================
+"""
+
+COMMSIGN = '#'
+
+PARAFORMAT = " {:<12s} = {:<24s} {:<s}\n"
+
+INCAR_PARAMETERS = {
+ # paraname defaultvalue paracomm
+ # GENERAL
+ "SYSTEM" : ["example" , (),
+ "system name"],
+ "NWRITE" : ["2" , (0, 1, 2, 3, 4),
+ "verbosity flag, 0|1|*2|3|4"],
+ "ISTART" : ["0" , (0, 1),
+ "0 New | 1 Restart"],
+ "ICHARG" : ["2" , (0, 1, 2, 4),
+ "0 orbital | 1 CHGCAR | *2 superposition | 4 POT"],
+ # parallel
+ "NPAR" : ["6" , (),
+ ""],
+ # MAGNETIC
+ "ISPIN" : ["2" , (1, 2),
+ "*1 no | 2 yes"],
+ "MAGMOM" : [" " , (),
+ "array, spin per atom"],
+ # WAVEFUNC
+ "INIWAV" : ["1" , (0, 1),
+ "0 jellium | *1 random"],
+ "LWAVE" : [".FALSE." , (".TRUE.", ".FALSE."),
+ "if write WAVECAR"],
+ # CHARGE
+ "LCHARG" : [".FALSE." , (".TRUE.", ".FALSE."),
+ "if write CHGCAR"],
+ # ELECTRONIC
+ "ENCUT" : ["450" , (),
+ "energy cutoff"],
+ "PREC" : ["Accurate" ,
+ ("Low", "Medium", "High", "Normal", "Accurate", "Single"),
+ "precision"],
+ "EDIFF" : ["1.0E-5" , (),
+ "stopping criterion for electronic updates"],
+ "NELM" : ["300" , (),
+ "maximium number of ionic updates"],
+ "NELMIN" : ["6" , (),
+ "minimium number of ionic updates"],
+ # IONIC
+ "EDIFFG" : ["-0.05" , (),
+ "stopping criterion for ionic updates"],
+ "NSW" : ["1000" , (),
+ "number of steps for ionic updates"],
+ "IBRION" : ["2" , (0,1,2,3,5),
+ "0 MD | 1 quasi-Newton | 2 CG | 3 damped-MD | 5 FC"],
+ "ISIF" : ["2" , (0, 1, 2, 3, 4, 5, 6),
+ "0 MD | *2 | 3 lat opt"],
+ "POTIM" : ["0.2" , (),
+ "ionic step size / MD time step"],
+ # Molecular Dynamics
+ "TEBEG" : ["300" , (),
+ "begin temperature"],
+ "TEEND" : ["300" , (),
+ "end temperature"],
+ "SMASS" : ["3" , (-3, -2, -1, 0, 3),
+ "controls velocities during AIMD"],
+ "NBLOCK" : ["10" , (),
+ "update XDATCAR every NBLOCK fs"],
+ # Smearing
+ "ISMEAR" : ["0" , (-5, 0, 1),
+ "-5 DOS | 0 large cell | 1 metal"],
+ "SIGMA" : ["0.05" , (),
+ "smearing parameter"],
+ # ALGO
+ "ALGO" : ["Fast" , ("ALL", "Normal", "Fast", "Very Fast"),
+ "algorithms for electronic self-consistent"],
+ "IALGO" : ["48" , (),
+ "8 CG | 48 RMM-DIIS"],
+ "LREAL" : ["Auto" , ("Auto", ".TRUE.", ".FALSE."),
+ "if calculation done in real spcae"],
+ "ISYM" : ["2" , (0, 1, 2, 3),
+ "0 off | 1 on | 2 charge | 3 no charge"],
+ # BAND
+ "LORBIT" : ["11" , (),
+ "PAW radii for projected DOS"],
+ "NEDOS" : ["2001" , (),
+ "DOSCAR points"],
+ # vdW
+ "IVDW" : ["11" , (),
+ "DFT-D3 without BJ damping"],
+ "VDW_s6" : ["1.0" , (),
+ "s6-scaling parameter (kept fix at 1.0)"],
+ "VDW_s8" : ["0.7875" , (),
+ "s8 for PBE"],
+ "VDW_a1" : ["0.4289" , (),
+ "a1 damping parameter for PBE"],
+ "VDW_a2" : ["4.4407" , (),
+ "a2 damping parameter for PBE"],
+ # DFT+U(J)
+ "LDAU" : [".TRUE." , (".TRUE.", ".FALSE."),
+ "Enable DFTU calculation"],
+ "LDAUTYPE" : ["2" , (1, 2, 4),
+ "1 Liechtenstein | *2 Dudarev | 4"], "LDAUL" : ["" , (),
+ "-1 off | 1 p | 2 d | 3 f"],
+ "LDAUU" : ["" , (),
+ "coulomb interaction"],
+ "LDAUJ" : ["" , (),
+ "exchange interaction"],
+ "LDAUPRINT" : ["2" , (0, 1, 2),
+ "*0 silent | 1 occupancy | 2 idem"],
+ "LMAXMIX" : ["4" , (2, 4, 6),
+ "twice the max l-quantum number"],
+ # Hybrid Functional
+ "LHFCALC" : [".TRUE." , (),
+ "Enable HF calculation"],
+ "AEXX" : ["0.25" , (),
+ "Hartree-Fock percentage"],
+ "PREFOCK" : ["Accurate" , (),
+ ""],
+ "LMAXFOCK" : ["4" , (4, 6),
+ "4 s/p | 6 f"],
+ "HFSCREEN" : ["0.2" , (),
+ "HSE06"],
+ "TIME" : ["0.4" , (),
+ ""],
+
+ }
+
+INCAR_PARACATEGORIES = {
+ # catname paranames
+ "GENERAL" : ["SYSTEM", "NWRITE", "ISTART"],
+ "PARALLEL" : ["NPAR"],
+ "WAVEFUNC" : ["INIWAV", "LWAVE"],
+ "CHARGE" : ["LCHARG"],
+ "MAGNETIC" : ["ISPIN"],
+ "ELECTRONIC": ["ENCUT", "PREC", "EDIFF", "NELM", "NELMIN"],
+ "IONIC" : ["EDIFFG", "NSW", "IBRION", "ISIF", "POTIM"],
+ "MD" : ["TEBEG", "TEEND", "SMASS", "NBLOCK"],
+ "SMEARING" : ["ISMEAR", "SIGMA"],
+ "VDW" : ["IVDW"],
+ "VDWBJ" : ["IVDW", "VDW_s6", "VDW_s8", "VDW_a1", "VDW_a2"],
+ "ALGO" : ["ALGO", "LREAL", "ISYM"],
+ "UJ" : ["LDAU", "LDAUTYPE", "LDAUU", "LDAUJ", "LDAUPRINT", "LMAXMIX"],
+ "HF" : ["LHFCALC", "AEXX", "PREFOCK", "LMAXFOCK", "HFSCREEN", "TIME"],
+ }
+
+BASIC_PARAS = ["GENERAL", "PARALLEL", "ELECTRONIC", "MAGNETIC", \
+ "SMEARING", "ALGO", "IONIC"]
+BUILTIN_PARASETS = {
+ # task paras specail settings
+ 'SC' : [BASIC_PARAS ,
+ []],
+ 'MD' : [["MD"] ,
+ [('IBRION', 0), ('ISIF', 0), ('POTIM', 1.0), ('NSW', 15000),
+ ('ALGO', 'Very Fast'), ('NELM', '60')]],
+ 'BAND' : [["BAND"] , []],
+ 'VDW' : [["VDW"] , []],
+ 'VDWBJ' : [["VDWBJ"] , []],
+ 'UJ' : [["UJ"] , []],
+ 'HF' : [["HF"] ,
+ [('ISYM', 3), ('ALGO', 'ALL')]],
+ }
+
From 1fe280a51fe73f99605d0e6a5c17895262b5ca17 Mon Sep 17 00:00:00 2001
From: jyxu <ahcigar@foxmail.com>
Date: Tue, 22 Oct 2019 20:50:54 +0100
Subject: [PATCH 2/5] Make *InCar* obeject default value as INCAR, compatable
with previous usage
---
vaspy/incar.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/vaspy/incar.py b/vaspy/incar.py
index 64a3fa4..b1a7244 100644
--- a/vaspy/incar.py
+++ b/vaspy/incar.py
@@ -326,7 +326,7 @@ def __repr__(self):
class InCar(Params):
- def __init__(self, src=None):
+ def __init__(self, src='INCAR'):
"""
Create a INCAR file class.
From df98ab70b5a73c49f63b50bc6fff765b69b61e21 Mon Sep 17 00:00:00 2001
From: jyxu <ahcigar@foxmail.com>
Date: Wed, 23 Oct 2019 10:29:50 +0100
Subject: [PATCH 3/5] add electronic mixing algo para in vasp_para_db.py
---
vaspy/vasp_para_db.py | 52 ++++++++++++++++++++++++++++++++++++++-----
1 file changed, 47 insertions(+), 5 deletions(-)
diff --git a/vaspy/vasp_para_db.py b/vaspy/vasp_para_db.py
index 0afb121..aedc31c 100644
--- a/vaspy/vasp_para_db.py
+++ b/vaspy/vasp_para_db.py
@@ -73,9 +73,20 @@
"TEEND" : ["300" , (),
"end temperature"],
"SMASS" : ["3" , (-3, -2, -1, 0, 3),
- "controls velocities during AIMD"],
+ "controls velocities in MD, -3 | -2 | -1 | >=0 Nosé"],
"NBLOCK" : ["10" , (),
"update XDATCAR every NBLOCK fs"],
+ # Advanced Molecualr Dynamics
+ "MDALGO" : ["21" , (0, 1, 2, 3, 11, 21, 13),
+ "0 standard MD | 21 meta Nose-Hoover"],
+ "LBLUEOUT" : [".FALSE." , (".TRUE.", ".FALSE."),
+ "print out free-energy gradient"],
+ # US
+ "HILLS_BIN" : ["15000" , (),
+ "bias potential update interval"],
+ # slow-grownth
+ "INCREM" : ["0" , (),
+ "increment in slow-grownth algo"],
# Smearing
"ISMEAR" : ["0" , (-5, 0, 1),
"-5 DOS | 0 large cell | 1 metal"],
@@ -90,6 +101,28 @@
"if calculation done in real spcae"],
"ISYM" : ["2" , (0, 1, 2, 3),
"0 off | 1 on | 2 charge | 3 no charge"],
+ "NSIM" : ["4" , (),
+ "blocked band update"],
+ # ALGO-Mixing
+ "IMIX" : ["4" , (),
+ "0 no mix | 1 Kerker | 2 Tchebycheff | 4 Broyden2"],
+ "AMIX" : ["0.4" , (),
+ "linear mixing parameter"],
+ "AMIN"
+ "BMIX" : ["1.0" , (),
+ "cutoff wave vector for Kerker mixing scheme"],
+ "AMIX_MAG" : ["1.6" , (),
+ "linear mixing parameter for magnetization"],
+ "BMIX_MAG" : ["1.0" , (),
+ ""],
+ "WC" : ["1000" , (),
+ "weight factor in each step in Broyden"],
+ "INIMIX" : ["1" , (),
+ "initial mixing in Broyden"],
+ "MIXPRE" : ["1" , (),
+ "preconditioning in Broyden"],
+ "MAXMIX" : ["-45" , (),
+ "maximum number steps stored in Broyden mixer"],
# BAND
"LORBIT" : ["11" , (),
"PAW radii for projected DOS"],
@@ -110,7 +143,8 @@
"LDAU" : [".TRUE." , (".TRUE.", ".FALSE."),
"Enable DFTU calculation"],
"LDAUTYPE" : ["2" , (1, 2, 4),
- "1 Liechtenstein | *2 Dudarev | 4"], "LDAUL" : ["" , (),
+ "1 Liechtenstein | *2 Dudarev | 4"],
+ "LDAUL" : ["" , (),
"-1 off | 1 p | 2 d | 3 f"],
"LDAUU" : ["" , (),
"coulomb interaction"],
@@ -133,7 +167,13 @@
"HSE06"],
"TIME" : ["0.4" , (),
""],
-
+ # POTCAR related
+ "POMASS" : ["" , (),
+ "mass each atomic species in a.u."],
+ "ZVAL" : ["" , (),
+ "valence for each atomic species"],
+ "RWIGS" : ["" , (),
+ "Wigner-Seitz radius"],
}
INCAR_PARACATEGORIES = {
@@ -161,8 +201,10 @@
'SC' : [BASIC_PARAS ,
[]],
'MD' : [["MD"] ,
- [('IBRION', 0), ('ISIF', 0), ('POTIM', 1.0), ('NSW', 15000),
- ('ALGO', 'Very Fast'), ('NELM', '60')]],
+ [('IBRION', 0), ('ISIF', 0), ('POTIM', 1.0), ('NSW', 15000),
+ ('PREC', 'Normal'), ('EDIFFG', -0.01),
+ ('ALGO', 'Very Fast'), ('ISYM', 0),
+ ('NELM', '120')]],
'BAND' : [["BAND"] , []],
'VDW' : [["VDW"] , []],
'VDWBJ' : [["VDWBJ"] , []],
From 2a9358b7a113e83fc67a0dd38161e27f3c65cb2b Mon Sep 17 00:00:00 2001
From: jyxu <ahcigar@foxmail.com>
Date: Wed, 23 Oct 2019 11:35:08 +0100
Subject: [PATCH 4/5] fix a bug which happens when no src is used when creating
*InCar* object
---
vaspy/incar.py | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/vaspy/incar.py b/vaspy/incar.py
index b1a7244..4858611 100644
--- a/vaspy/incar.py
+++ b/vaspy/incar.py
@@ -342,6 +342,10 @@ def __init__(self, src='INCAR'):
============ =======================================
"""
# super(self.__class__, self).__init__(src)
+ if src == 'INCAR':
+ if not os.path.exists('INCAR'):
+ src = None
+
if src is None:
self.paras = ()
else:
@@ -352,7 +356,8 @@ def __init__(self, src='INCAR'):
elif isinstance(src, Params):
self.paras = src.paras
- self.paras = self.remove_duplicates(self.paras)
+ if self.paras != ():
+ self.paras = self.remove_duplicates(self.paras)
self.parasets = None
# set logger
From f74184818645df99a510933e1a1cee4c0fde003d Mon Sep 17 00:00:00 2001
From: hsulab <ahcigar@foxmail.com>
Date: Wed, 29 Jul 2020 22:31:27 +0100
Subject: [PATCH 5/5] update few parameters used in INCAR
---
vaspy/incar.py | 4 +++-
vaspy/vasp_para_db.py | 23 ++++++++++++++++-------
2 files changed, 19 insertions(+), 8 deletions(-)
diff --git a/vaspy/incar.py b/vaspy/incar.py
index 4858611..7d8ae6f 100644
--- a/vaspy/incar.py
+++ b/vaspy/incar.py
@@ -426,10 +426,12 @@ def quickgen(self, tasks, **kargs):
"""Quick generation of INCAR with built-in parameters."""
# check task
tasks = tasks.strip().split('-')
+
+ # check if SC in tasks
task_basic = ['SC']
if 'SC' not in tasks:
task_basic.extend(tasks)
- tasks = task_basic
+ tasks = task_basic
parasets = []
for task in tasks:
diff --git a/vaspy/vasp_para_db.py b/vaspy/vasp_para_db.py
index aedc31c..30053d9 100644
--- a/vaspy/vasp_para_db.py
+++ b/vaspy/vasp_para_db.py
@@ -30,7 +30,9 @@
"0 orbital | 1 CHGCAR | *2 superposition | 4 POT"],
# parallel
"NPAR" : ["6" , (),
- ""],
+ "NCORE=ncores/NPAR"],
+ "NCORE" : ["8" , (),
+ "cores/orbital, Better use NPAR"],
# MAGNETIC
"ISPIN" : ["2" , (1, 2),
"*1 no | 2 yes"],
@@ -39,11 +41,12 @@
# WAVEFUNC
"INIWAV" : ["1" , (0, 1),
"0 jellium | *1 random"],
- "LWAVE" : [".FALSE." , (".TRUE.", ".FALSE."),
- "if write WAVECAR"],
# CHARGE
+ # Writing
"LCHARG" : [".FALSE." , (".TRUE.", ".FALSE."),
"if write CHGCAR"],
+ "LWAVE" : [".FALSE." , (".TRUE.", ".FALSE."),
+ "if write WAVECAR"],
# ELECTRONIC
"ENCUT" : ["450" , (),
"energy cutoff"],
@@ -56,6 +59,12 @@
"maximium number of ionic updates"],
"NELMIN" : ["6" , (),
"minimium number of ionic updates"],
+ # dipole correction
+ "IDIPOL" : ["3" , (),
+ "surface 3"],
+ # hole/electron
+ "NELECT" : ["0" , (),
+ "number of electrons"],
# IONIC
"EDIFFG" : ["-0.05" , (),
"stopping criterion for ionic updates"],
@@ -179,9 +188,9 @@
INCAR_PARACATEGORIES = {
# catname paranames
"GENERAL" : ["SYSTEM", "NWRITE", "ISTART"],
+ "WRITING" : ["LCHARG", "LWAVE"],
"PARALLEL" : ["NPAR"],
- "WAVEFUNC" : ["INIWAV", "LWAVE"],
- "CHARGE" : ["LCHARG"],
+ "WAVEFUNC" : ["INIWAV"],
"MAGNETIC" : ["ISPIN"],
"ELECTRONIC": ["ENCUT", "PREC", "EDIFF", "NELM", "NELMIN"],
"IONIC" : ["EDIFFG", "NSW", "IBRION", "ISIF", "POTIM"],
@@ -190,11 +199,11 @@
"VDW" : ["IVDW"],
"VDWBJ" : ["IVDW", "VDW_s6", "VDW_s8", "VDW_a1", "VDW_a2"],
"ALGO" : ["ALGO", "LREAL", "ISYM"],
- "UJ" : ["LDAU", "LDAUTYPE", "LDAUU", "LDAUJ", "LDAUPRINT", "LMAXMIX"],
+ "UJ" : ["LDAU", "LDAUTYPE", "LDAUL", "LDAUU", "LDAUJ", "LDAUPRINT", "LMAXMIX"],
"HF" : ["LHFCALC", "AEXX", "PREFOCK", "LMAXFOCK", "HFSCREEN", "TIME"],
}
-BASIC_PARAS = ["GENERAL", "PARALLEL", "ELECTRONIC", "MAGNETIC", \
+BASIC_PARAS = ["GENERAL", "WRITING", "PARALLEL", "ELECTRONIC", "MAGNETIC", \
"SMEARING", "ALGO", "IONIC"]
BUILTIN_PARASETS = {
# task paras specail settings