Source code for ase.calculators.cp2k

# -*- coding: utf-8 -*-

"""This module defines an ASE interface to CP2K.

http://www.cp2k.org
Author: Ole Schuett <ole.schuett@mat.ethz.ch>
"""

from __future__ import print_function

import os
import os.path
from warnings import warn
from subprocess import Popen, PIPE
import numpy as np
import ase.io
from ase.units import Rydberg
from ase.calculators.calculator import Calculator, all_changes, Parameters


[docs]class CP2K(Calculator): """ASE-Calculator for CP2K. CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. It provides a general framework for different methods such as e.g., density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) and classical pair and many-body potentials. CP2K is freely available under the GPL license. It is written in Fortran 2003 and can be run efficiently in parallel. Check http://www.cp2k.org about how to obtain and install CP2K. Make sure that you also have the CP2K-shell available, since it is required by the CP2K-calulator. The CP2K-calculator relies on the CP2K-shell. The CP2K-shell was originally designed for interactive sessions. When a calculator object is instantiated, it launches a CP2K-shell as a subprocess in the background and communications with it through stdin/stdout pipes. This has the advantage that the CP2K process is kept alive for the whole lifetime of the calculator object, i.e. there is no startup overhead for a sequence of energy evaluations. Furthermore, the usage of pipes avoids slow file- system I/O. This mechanism even works for MPI-parallelized runs, because stdin/stdout of the first rank are forwarded by the MPI-environment to the mpiexec-process. The command used by the calculator to launch the CP2K-shell is ``cp2k_shell``. To run a parallelized simulation use something like this: >>> CP2K.command="env OMP_NUM_THREADS=2 mpiexec -np 4 cp2k_shell.psmp" Arguments: auto_write: bool Flag to enable the auto-write mode. If enabled the ``write()`` routine is called after every calculation, which mimics the behavior of the ``FileIOCalculator``. Default is ``False``. basis_set: str Name of the basis set to be use. The default is ``DZVP-MOLOPT-SR-GTH``. basis_set_file: str Filename of the basis set file. Default is ``BASIS_MOLOPT``. Set the environment variable $CP2K_DATA_DIR to enabled automatic file discovered. charge: float The total charge of the system. Default is ``0``. command: str The command used to launch the CP2K-shell. If ``command`` is not passed as an argument to the constructor, the class-variable ``CP2K.command``, and then the environment variable ``$ASE_CP2K_COMMAND`` are checked. Eventually, ``cp2k_shell`` is used as default. cutoff: float The cutoff of the finest grid level. Default is ``400 * Rydberg``. debug: bool Flag to enable debug mode. This will print all communication between the CP2K-shell and the CP2K-calculator. Default is ``False``. force_eval_method: str The method CP2K uses to evaluate energies and forces. The default is ``Quickstep``, which is CP2K's module for electronic structure methods like DFT. inp: str CP2K input template. If present, the calculator will augment the template, e.g. with coordinates, and use it to launch CP2K. Hence, this generic mechanism gives access to all features of CP2K. Note, that most keywords accept ``None`` to disable the generation of the corresponding input section. max_scf: int Maximum number of SCF iteration to be performed for one optimization. Default is ``50``. poisson_solver: str The poisson solver to be used. Currently, the only supported values are ``auto`` and ``None``. Default is ``auto``. potential_file: str Filename of the pseudo-potential file. Default is ``POTENTIAL``. Set the environment variable $CP2K_DATA_DIR to enabled automatic file discovered. pseudo_potential: str Name of the pseudo-potential to be use. Default is ``auto``. This tries to infer the potential from the employed XC-functional, otherwise it falls back to ``GTH-PBE``. stress_tensor: bool Indicates whether the analytic stress-tensor should be calculated. Default is ``True``. uks: bool Requests an unrestricted Kohn-Sham calculations. This is need for spin-polarized systems, ie. with an odd number of electrons. Default is ``False``. xc: str Name of exchange and correlation functional. Accepts all functions supported by CP2K itself or libxc. Default is ``LDA``. print_level: str PRINT_LEVEL of global output. Possible options are: DEBUG Everything is written out, useful for debugging purposes only HIGH Lots of output LOW Little output MEDIUM Quite some output SILENT Almost no output Default is 'LOW' """ implemented_properties = ['energy', 'free_energy', 'forces', 'stress'] command = None default_parameters = dict( auto_write=False, basis_set='DZVP-MOLOPT-SR-GTH', basis_set_file='BASIS_MOLOPT', charge=0, cutoff=400 * Rydberg, force_eval_method="Quickstep", inp='', max_scf=50, potential_file='POTENTIAL', pseudo_potential='auto', stress_tensor=True, uks=False, poisson_solver='auto', xc='LDA', print_level='LOW') def __init__(self, restart=None, ignore_bad_restart_file=False, label='cp2k', atoms=None, command=None, debug=False, **kwargs): """Construct CP2K-calculator object.""" self._debug = debug self._force_env_id = None self._shell = None self.label = None self.parameters = None self.results = None self.atoms = None # Several places are check to determine self.command if command is not None: self.command = command elif CP2K.command is not None: self.command = CP2K.command elif 'ASE_CP2K_COMMAND' in os.environ: self.command = os.environ['ASE_CP2K_COMMAND'] else: self.command = 'cp2k_shell' # default Calculator.__init__(self, restart=restart, ignore_bad_restart_file=ignore_bad_restart_file, label=label, atoms=atoms, **kwargs) self._shell = Cp2kShell(self.command, self._debug) if restart is not None: try: self.read(restart) except: if ignore_bad_restart_file: self.reset() else: raise def __del__(self): """Release force_env and terminate cp2k_shell child process""" if self._shell: self._release_force_env() del(self._shell) def set(self, **kwargs): """Set parameters like set(key1=value1, key2=value2, ...).""" changed_parameters = Calculator.set(self, **kwargs) if changed_parameters: self.reset() def write(self, label): 'Write atoms, parameters and calculated results into restart files.' if self._debug: print("Writting restart to: ", label) self.atoms.write(label + '_restart.traj') self.parameters.write(label + '_params.ase') from ase.io.jsonio import write_json with open(label + '_results.json', 'w') as fd: write_json(fd, self.results) def read(self, label): 'Read atoms, parameters and calculated results from restart files.' self.atoms = ase.io.read(label + '_restart.traj') self.parameters = Parameters.read(label + '_params.ase') from ase.io.jsonio import read_json with open(label + '_results.json') as fd: self.results = read_json(fd) def calculate(self, atoms=None, properties=None, system_changes=all_changes): """Do the calculation.""" if not properties: properties = ['energy'] Calculator.calculate(self, atoms, properties, system_changes) if self._debug: print("system_changes:", system_changes) if 'numbers' in system_changes: self._release_force_env() if self._force_env_id is None: self._create_force_env() # enable eV and Angstrom as units self._shell.send('UNITS_EV_A') self._shell.expect('* READY') n_atoms = len(self.atoms) if 'cell' in system_changes: cell = self.atoms.get_cell() self._shell.send('SET_CELL %d' % self._force_env_id) for i in range(3): self._shell.send('%.18e %.18e %.18e' % tuple(cell[i, :])) self._shell.expect('* READY') if 'positions' in system_changes: self._shell.send('SET_POS %d' % self._force_env_id) self._shell.send('%d' % (3 * n_atoms)) for pos in self.atoms.get_positions(): self._shell.send('%.18e %.18e %.18e' % tuple(pos)) self._shell.send('*END') max_change = float(self._shell.recv()) assert max_change >= 0 # sanity check self._shell.expect('* READY') self._shell.send('EVAL_EF %d' % self._force_env_id) self._shell.expect('* READY') self._shell.send('GET_E %d' % self._force_env_id) self.results['energy'] = float(self._shell.recv()) self.results['free_energy'] = self.results['energy'] self._shell.expect('* READY') forces = np.zeros(shape=(n_atoms, 3)) self._shell.send('GET_F %d' % self._force_env_id) nvals = int(self._shell.recv()) assert nvals == 3 * n_atoms # sanity check for i in range(n_atoms): line = self._shell.recv() forces[i, :] = [float(x) for x in line.split()] self._shell.expect('* END') self._shell.expect('* READY') self.results['forces'] = forces self._shell.send('GET_STRESS %d' % self._force_env_id) line = self._shell.recv() self._shell.expect('* READY') stress = np.array([float(x) for x in line.split()]).reshape(3, 3) assert np.all(stress == np.transpose(stress)) # should be symmetric # Convert 3x3 stress tensor to Voigt form as required by ASE stress = np.array([stress[0, 0], stress[1, 1], stress[2, 2], stress[1, 2], stress[0, 2], stress[0, 1]]) self.results['stress'] = -1.0 * stress # cp2k uses the opposite sign if self.parameters.auto_write: self.write(self.label) def _create_force_env(self): """Instantiates a new force-environment""" assert self._force_env_id is None label_dir = os.path.dirname(self.label) if len(label_dir) > 0 and not os.path.exists(label_dir): print('Creating directory: ' + label_dir) os.makedirs(label_dir) # cp2k expects dirs to exist inp = self._generate_input() inp_fn = self.label + '.inp' out_fn = self.label + '.out' self._write_file(inp_fn, inp) self._shell.send('LOAD %s %s' % (inp_fn, out_fn)) self._force_env_id = int(self._shell.recv()) assert self._force_env_id > 0 self._shell.expect('* READY') def _write_file(self, fn, content): """Write content to a file""" if self._debug: print('Writting to file: ' + fn) print(content) if self._shell.version < 2.0: f = open(fn, 'w') f.write(content) f.close() else: lines = content.split('\n') if self._shell.version < 2.1: lines = [l.strip() for l in lines] # save chars self._shell.send('WRITE_FILE') self._shell.send(fn) self._shell.send('%d' % len(lines)) for line in lines: self._shell.send(line) self._shell.send('*END') self._shell.expect('* READY') def _release_force_env(self): """Destroys the current force-environment""" if self._force_env_id: if self._shell.isready: self._shell.send('DESTROY %d' % self._force_env_id) self._shell.expect('* READY') else: msg = "CP2K-shell not ready, could not release force_env." warn(msg, RuntimeWarning) self._force_env_id = None def _generate_input(self): """Generates a CP2K input file""" p = self.parameters root = parse_input(p.inp) root.add_keyword('GLOBAL', 'PROJECT ' + self.label) if p.print_level: root.add_keyword('GLOBAL', 'PRINT_LEVEL ' + p.print_level) if p.force_eval_method: root.add_keyword('FORCE_EVAL', 'METHOD ' + p.force_eval_method) if p.stress_tensor: root.add_keyword('FORCE_EVAL', 'STRESS_TENSOR ANALYTICAL') root.add_keyword('FORCE_EVAL/PRINT/STRESS_TENSOR', '_SECTION_PARAMETERS_ ON') if p.basis_set_file: root.add_keyword('FORCE_EVAL/DFT', 'BASIS_SET_FILE_NAME ' + p.basis_set_file) if p.potential_file: root.add_keyword('FORCE_EVAL/DFT', 'POTENTIAL_FILE_NAME ' + p.potential_file) if p.cutoff: root.add_keyword('FORCE_EVAL/DFT/MGRID', 'CUTOFF [eV] %.18e' % p.cutoff) if p.max_scf: root.add_keyword('FORCE_EVAL/DFT/SCF', 'MAX_SCF %d' % p.max_scf) root.add_keyword('FORCE_EVAL/DFT/LS_SCF', 'MAX_SCF %d' % p.max_scf) if p.xc: legacy_libxc = "" for functional in p.xc.split(): functional = functional.replace("LDA", "PADE") # resolve alias xc_sec = root.get_subsection('FORCE_EVAL/DFT/XC/XC_FUNCTIONAL') # libxc input section changed over time if functional.startswith("XC_") and self._shell.version < 3.0: legacy_libxc += " " + functional # handled later elif functional.startswith("XC_"): s = InputSection(name='LIBXC') s.keywords.append('FUNCTIONAL ' + functional) xc_sec.subsections.append(s) else: s = InputSection(name=functional.upper()) xc_sec.subsections.append(s) if legacy_libxc: root.add_keyword('FORCE_EVAL/DFT/XC/XC_FUNCTIONAL/LIBXC', 'FUNCTIONAL ' + legacy_libxc) if p.uks: root.add_keyword('FORCE_EVAL/DFT', 'UNRESTRICTED_KOHN_SHAM ON') if p.charge and p.charge != 0: root.add_keyword('FORCE_EVAL/DFT', 'CHARGE %d' % p.charge) # add Poisson solver if needed if p.poisson_solver == 'auto' and not any(self.atoms.get_pbc()): root.add_keyword('FORCE_EVAL/DFT/POISSON', 'PERIODIC NONE') root.add_keyword('FORCE_EVAL/DFT/POISSON', 'PSOLVER MT') # write coords syms = self.atoms.get_chemical_symbols() atoms = self.atoms.get_positions() for elm, pos in zip(syms, atoms): line = '%s %.18e %.18e %.18e' % (elm, pos[0], pos[1], pos[2]) root.add_keyword('FORCE_EVAL/SUBSYS/COORD', line, unique=False) # write cell pbc = ''.join([a for a, b in zip('XYZ', self.atoms.get_pbc()) if b]) if len(pbc) == 0: pbc = 'NONE' root.add_keyword('FORCE_EVAL/SUBSYS/CELL', 'PERIODIC ' + pbc) c = self.atoms.get_cell() for i, a in enumerate('ABC'): line = '%s %.18e %.18e %.18e' % (a, c[i, 0], c[i, 1], c[i, 2]) root.add_keyword('FORCE_EVAL/SUBSYS/CELL', line) # determine pseudo-potential potential = p.pseudo_potential if p.pseudo_potential == 'auto': if p.xc and p.xc.upper() in ('LDA', 'PADE', 'BP', 'BLYP', 'PBE',): potential = 'GTH-' + p.xc.upper() else: msg = 'No matching pseudo potential found, using GTH-PBE' warn(msg, RuntimeWarning) potential = 'GTH-PBE' # fall back # write atomic kinds subsys = root.get_subsection('FORCE_EVAL/SUBSYS').subsections kinds = dict([(s.params, s) for s in subsys if s.name == "KIND"]) for elem in set(self.atoms.get_chemical_symbols()): if elem not in kinds.keys(): s = InputSection(name='KIND', params=elem) subsys.append(s) kinds[elem] = s if p.basis_set: kinds[elem].keywords.append('BASIS_SET ' + p.basis_set) if potential: kinds[elem].keywords.append('POTENTIAL ' + potential) output_lines = ['!!! Generated by ASE !!!'] + root.write() return '\n'.join(output_lines)
class Cp2kShell(object): """Wrapper for CP2K-shell child-process""" def __init__(self, command, debug): """Construct CP2K-shell object""" self.isready = False self.version = 1.0 # assume oldest possible version until verified self._child = None self._debug = debug # launch cp2k_shell child process assert 'cp2k_shell' in command if self._debug: print(command) self._child = Popen(command, shell=True, universal_newlines=True, stdin=PIPE, stdout=PIPE, bufsize=1) self.expect('* READY') # check version of shell self.send('VERSION') line = self.recv() if not line.startswith('CP2K Shell Version:'): raise RuntimeError('Cannot determine version of CP2K shell. ' 'Probably the shell version is too old. ' 'Please update to CP2K 3.0 or newer.') shell_version = line.rsplit(":", 1)[1] self.version = float(shell_version) assert self.version >= 1.0 self.expect('* READY') # enable harsh mode, stops on any error self.send('HARSH') self.expect('* READY') def __del__(self): """Terminate cp2k_shell child process""" if self.isready: self.send('EXIT') rtncode = self._child.wait() assert rtncode == 0 # child process exited properly? else: warn("CP2K-shell not ready, sending SIGTERM.", RuntimeWarning) self._child.terminate() self._child = None self.version = None self.isready = False def send(self, line): """Send a line to the cp2k_shell""" assert self._child.poll() is None # child process still alive? if self._debug: print('Sending: ' + line) if self.version < 2.1 and len(line) >= 80: raise Exception('Buffer overflow, upgrade CP2K to r16779 or later') assert(len(line) < 800) # new input buffer size self.isready = False self._child.stdin.write(line + '\n') def recv(self): """Receive a line from the cp2k_shell""" assert self._child.poll() is None # child process still alive? line = self._child.stdout.readline().strip() if self._debug: print('Received: ' + line) self.isready = line == '* READY' return line def expect(self, line): """Receive a line and asserts that it matches the expected one""" received = self.recv() assert received == line class InputSection(object): """Represents a section of a CP2K input file""" def __init__(self, name, params=None): self.name = name.upper() self.params = params self.keywords = [] self.subsections = [] def write(self): """Outputs input section as string""" output = [] for k in self.keywords: output.append(k) for s in self.subsections: if s.params: output.append('&%s %s' % (s.name, s.params)) else: output.append('&%s' % s.name) for l in s.write(): output.append(' %s' % l) output.append('&END %s' % s.name) return output def add_keyword(self, path, line, unique=True): """Adds a keyword to section.""" parts = path.upper().split('/', 1) candidates = [s for s in self.subsections if s.name == parts[0]] if len(candidates) == 0: s = InputSection(name=parts[0]) self.subsections.append(s) candidates = [s] elif len(candidates) != 1: raise Exception('Multiple %s sections found ' % parts[0]) key = line.split()[0].upper() if len(parts) > 1: candidates[0].add_keyword(parts[1], line, unique) elif key == '_SECTION_PARAMETERS_': if candidates[0].params is not None: msg = 'Section parameter of section %s already set' % parts[0] raise Exception(msg) candidates[0].params = line.split(' ', 1)[1].strip() else: old_keys = [k.split()[0].upper() for k in candidates[0].keywords] if unique and key in old_keys: msg = 'Keyword %s already present in section %s' raise Exception(msg % (key, parts[0])) candidates[0].keywords.append(line) def get_subsection(self, path): """Finds a subsection""" parts = path.upper().split('/', 1) candidates = [s for s in self.subsections if s.name == parts[0]] if len(candidates) > 1: raise Exception('Multiple %s sections found ' % parts[0]) if len(candidates) == 0: s = InputSection(name=parts[0]) self.subsections.append(s) candidates = [s] if len(parts) == 1: return candidates[0] return candidates[0].get_subsection(parts[1]) def parse_input(inp): """Parses the given CP2K input string""" root_section = InputSection('CP2K_INPUT') section_stack = [root_section] for line in inp.split('\n'): line = line.split('!', 1)[0].strip() if len(line) == 0: continue if line.upper().startswith('&END'): s = section_stack.pop() elif line[0] == '&': parts = line.split(' ', 1) name = parts[0][1:] if len(parts) > 1: s = InputSection(name=name, params=parts[1].strip()) else: s = InputSection(name=name) section_stack[-1].subsections.append(s) section_stack.append(s) else: section_stack[-1].keywords.append(line) return root_section