analysis folder

.gitignore

@@ -0,0 +1,10 @@
+__pycache__/
+*.pyc
+.vs/
+.ipynb_checkpoints/
+.idea/
+
+*.db
+*.traj
+*.txt
+*.json

.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+repos:
+-   repo: https://github.com/ambv/black
+    rev: stable
+    hooks:
+    - id: black
+      language_version: python3.9
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    - id: flake8
+    - id: trailing-whitespace
+    - id: check-added-large-files
+    - id: end-of-file-fixer

00_make_molecule.py

@@ -1,13 +1,13 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-import numpy as np  
+import numpy as np
 from ase.build import molecule
-from ase.visualize import view 
+from ase.visualize import view
 import ase.io as io
 
-atoms = molecule('H2O')
-atoms.set_cell(8*np.identity(3))
+atoms = molecule("H2O")
+atoms.set_cell(8 * np.identity(3))
 atoms.center()
 view(atoms)
-io.write('start.traj', atoms)
+io.write("start.traj", atoms)

01_submit_job.py

@@ -1,43 +1,43 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-#SBATCH -p high
-#SBATCH --job-name=opt_try
-#SBATCH --output=job.out
-#SBATCH --error=job.err
-#SBATCH --time=8:00:00
-#SBATCH --nodes=1
-#SBATCH --ntasks-per-node=16
-#SiBATCH --exclusive
+# SBATCH -p high
+# SBATCH --job-name=opt_try
+# SBATCH --output=job.out
+# SBATCH --error=job.err
+# SBATCH --time=8:00:00
+# SBATCH --nodes=1
+# SBATCH --ntasks-per-node=16
+# SiBATCH --exclusive
 
 """
 Created on Thu Mar 26 17:10:56 2020
 
 @author: ark245
 """
-import os, sys 
-sys.path.insert(0,'/home/ark245/lib/onboarding_DFT/')
+import os, sys
+
+sys.path.insert(0, "/home/ark245/lib/onboarding_DFT/")
 from ase import io
 from kul_tools import KulTools as KT
 
-kt = KT(gamma_only=False,structure_type='zeo')
-kt.set_calculation_type('opt')
-atoms = io.read('start.traj')
-atoms.pbc=True
+kt = KT(gamma_only=False, structure_type="zeo")
+kt.set_calculation_type("opt")
+atoms = io.read("start.traj")
+atoms.pbc = True
 kt.set_structure(atoms)
-kt.set_overall_vasp_params({'gga':'RP'})
+kt.set_overall_vasp_params({"gga": "RP"})
 kt.run()
 
 
-#print(kt.calc_default.int_params['ismear'])
-#print(kt.calc_default.special_params['lreal'])
-#print(kt.calculation_type)
-
+# print(kt.calc_default.int_params['ismear'])
+# print(kt.calc_default.special_params['lreal'])
+# print(kt.calculation_type)
 
-# Calculation type 
-# opt --> needs atoms 
-# opt_fine --> needs constraints 
-# vib --> needs constraints 
-# dimer --> needs path annd atoms 
-# neb --> needs traj 
 
+# Calculation type
+# opt --> needs atoms
+# opt_fine --> needs constraints
+# vib --> needs constraints
+# dimer --> needs path annd atoms
+# neb --> needs traj

05_dimer_demo.py

@@ -1,26 +1,27 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-#SBATCH -p high
-#SBATCH --job-name=opt_try
-#SBATCH --output=job.out
-#SBATCH --error=job.err
-#SBATCH --time=8:00:00
-#SBATCH --nodes=1
-#SBATCH --ntasks-per-node=64 -c 2
-#SiBATCH --exclusive
+# SBATCH -p high
+# SBATCH --job-name=opt_try
+# SBATCH --output=job.out
+# SBATCH --error=job.err
+# SBATCH --time=8:00:00
+# SBATCH --nodes=1
+# SBATCH --ntasks-per-node=64 -c 2
+# SiBATCH --exclusive
 
 """
 Created on Thu Mar 26 17:10:56 2020
 @author: ark245
 """
 import os, sys
-sys.path.insert(0,'/home/ark245/lib/onboarding_DFT/')
+
+sys.path.insert(0, "/home/ark245/lib/onboarding_DFT/")
 from ase import io
 from kul_tools import KulTools as KT
 
-kt = KT(gamma_only=False,structure_type='zeo',calculation_type='dimer')
-atoms = io.read('dimer_start.traj')
+kt = KT(gamma_only=False, structure_type="zeo", calculation_type="dimer")
+atoms = io.read("dimer_start.traj")
 kt.set_structure(atoms)
-kt.set_overall_vasp_params({'gga':'RP'})
+kt.set_overall_vasp_params({"gga": "RP"})
 kt.run()

KulTools/KT_object.py

@@ -0,0 +1,142 @@
+"""class structure(custom_params,ase_atoms)
+    assert param has been Changed
+    ISMEAR SIGMA etc
+    structure.get_calc_object (VASP,QE)
+    structure.set_defaults
+
+class calculation_type(custom_params):
+    self.params = {}
+    self.params["IBRION"] = self.custom
+    contains default params for each calc
+    if calculator_name - 'VASP':
+        kt_params = ""
+    else assert
+assert param has been Changed
+IBRION,NSW,EDIFFG,POTIM
+
+
+from kt.calculation_type import calc_params...
+
+.sh script package -> environments"""
+
+from kt_structure import KT_structure
+from ase.calculators.vasp import Vasp
+from load_environ import identify_hpc_cluster, identify_vasp_environ
+
+
+class KT_Object(KT_structure):
+    def __init__(
+        self,
+        gamma_only,
+        structure,
+        structure_type,
+        calculator_name,
+        calculation_type,
+        calc_params={},
+    ):
+
+        super().__init__(structure, structure_type, calculator_name, calculation_type)
+
+        self.gamma = gamma_only
+        self.user_params = calc_params
+        self.kt_params = {}
+
+        self._set_environment_variables()
+
+        if self.calc_name.lower() == "vasp":
+            self._load_structure_type_params_vasp()
+            self._load_calc_type_params_vasp()
+
+        self._load_update_kt_params()
+
+        self._init_ase_calc()
+
+    def _set_environment_variables(self):
+        if self.calc_name.lower() == "vasp":
+            self.hpc = identify_hpc_cluster()
+            print("ENVIRONMENT VARIABLES ARE AT:")
+            print(identify_vasp_environ(self.hpc, self.gamma))
+
+        else:
+            pass
+
+    def _load_structure_type_params_vasp(self):
+
+        if self.structure_type.lower() == "metal":
+            self.default_calc_params.update({"sigma": 0.2, "ismear": 1})
+
+        elif self.structure_type.lower() == "gas-phase":
+            self.default_calc_params.update({"lreal": False})
+
+        else:
+            pass
+
+    def _load_calc_type_params_vasp(self):
+
+        if self.calculation_type.lower() == "spe":
+            self.default_calc_params.update({"nsw": 0})
+
+        elif self.calculation_type.lower() == "opt_fine":
+            self.default_calc_params.update(
+                {"ibrion": 1, "potim": 0.05, "nsw": 50, "ediffg": -0.03}
+            )
+
+        elif self.calculation_type.lower() == "vib":
+            self.default_calc_params.update({"ibrion": 5, "potim": 0.02, "nsw": 1})
+
+        elif self.calculation_type.lower() == "solv":
+            self.default_calc_params.update(
+                {
+                    "potim": 0.0,
+                    "nsw": 5,
+                    "lwave": True,
+                    "lsol": False,
+                    "prec": "Accurate",
+                }
+            )
+
+        elif self.calculation_type.lower() == "solv-spe":
+            self.default_calc_params.update(
+                {
+                    "potim": 0.0,
+                    "nsw": 3,
+                    "lwave": True,
+                    "lsol": True,
+                    "prec": "Accurate",
+                }
+            )
+
+        elif self.calculation_type.lower() == "solv-spe-rho":
+            self.default_calc_params.update(
+                {
+                    "potim": 0.0,
+                    "nsw": 5,
+                    "lrho": True,
+                    "lwave": True,
+                    "lsol": True,
+                    "prec": "Accurate",
+                    "lrhob": True,
+                    "lrhoion": True,
+                }
+            )
+
+        elif self.calculation_type.lower() == "md":
+            self.default_calc_params.update(
+                {"ibrion": 0, "nsw": 1000000, "tebeg": 298, "isif": 2, "smass": 0}
+            )
+
+        else:
+            pass
+
+    def _load_update_kt_params(self):
+        self.default_calc_params.update(self.user_params)
+        self.kt_params = self.default_calc_params
+
+    def _init_ase_calc(self):
+        if self.calc_name.lower() == "vasp":
+            self.ase_calculator = Vasp()
+        else:
+            pass
+
+        for key in self.kt_params:
+            self.ase_calculator.set(key=self.kt_params[key])

KulTools/README.md

@@ -0,0 +1 @@
+Script related to creating the kT object

KulTools/calc_object.py

@@ -0,0 +1,43 @@
+from ase.calculators.vasp import Vasp
+
+
+class default_calc:
+    def __init__(self):
+        pass
+
+    def load_default_vasp(self):
+        self.vasp_params = {
+            "kpts": (1, 1, 1),
+            "potim": 0.5,
+            "encut": 500,
+            "ispin": 2,
+            "nsw": 50,
+            "prec": "Normal",
+            "istart": 1,
+            "isif": 2,
+            "ismear": 0,
+            "sigma": 0.05,
+            "nelmin": 4,
+            "nelmdl": -4,
+            "nwrite": 1,
+            "icharg": 2,
+            "lasph": True,
+            "ediff": 1e-6,
+            "ediffg": -0.05,
+            "ibrion": 2,
+            "lcharg": False,
+            "lwave": False,
+            "laechg": False,
+            "voskown": 1,
+            "algo": "Fast",
+            "lplane": True,
+            "lreal": "Auto",
+            "isym": 0,
+            "xc": "PBE",
+            "lorbit": 11,
+            "nupdown": -1,
+            "npar": 4,
+            "nsim": 4,
+            "ivdw": 12,
+        }
+        return self.vasp_params