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# Psi4: an open-source quantum chemistry software package
# Copyright (c) 2007-2018 The Psi4 Developers.
# The copyrights for code used from other parties are included in
# the corresponding files.
# This file is part of Psi4.
# Psi4 is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, version 3.
# Psi4 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# GNU Lesser General Public License for more details.
# You should have received a copy of the GNU Lesser General Public License along
# with Psi4; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
import atexit
import sys
import os
import json
import datetime
import argparse
from argparse import RawTextHelpFormatter
# yapf: disable
parser = argparse.ArgumentParser(description="Psi4: Open-Source Quantum Chemistry", formatter_class=RawTextHelpFormatter)
parser.add_argument("-i", "--input", default="input.dat",
help="Input file name. Default: input.dat.")
parser.add_argument("-o", "--output", help="""\
Redirect output elsewhere.
Default: when input filename is 'input.dat', 'output.dat'.
Otherwise, output filename defaults to input filename with
any '.in' or 'dat' extension replaced by '.out'""")
parser.add_argument("-a", "--append", action='store_true',
help="Appends results to output file. Default: Truncate first")
parser.add_argument("-V", "--version", action='store_true',
help="Prints version information.")
parser.add_argument("-n", "--nthread", default=1,
help="Number of threads to use. Psi4 disregards OMP_NUM_THREADS/MKL_NUM_THREADS.")
parser.add_argument("-s", "--scratch",
help="Scratch directory to use. Overrides PSI_SCRATCH.")
parser.add_argument("-m", "--messy", action='store_true',
help="Leaves temporary files after the run is completed.")
# parser.add_argument("-d", "--debug", action='store_true', help="Flush the outfile at every print statement.")
# parser.add_argument("-r", "--restart", action='store_true', help="Number to be used instead of process id.")
parser.add_argument("-p", "--prefix",
help="Prefix name for psi files. Default psi")
parser.add_argument("--psiapi-path", action='store_true',
help="""Generates a bash command to source correct Python """
"""interpreter and path for ``python -c "import psi4"``""")
parser.add_argument("-v", "--verbose", action='store_true', help="Prints Psithon to Python translation.")
parser.add_argument("--inplace", action='store_true',
help="Runs Psi4 from the source directory. !Warning! expert option.")
parser.add_argument("-l", "--psidatadir",
help="Specifies where to look for the Psi4 data directory. Overrides PSIDATADIR. !Warning! expert option.")
parser.add_argument("-k", "--skip-preprocessor", action='store_true',
help="Skips input preprocessing. !Warning! expert option.")
parser.add_argument("--json", action='store_true',
help="Runs a JSON input file. !Warning! experimental option.")
parser.add_argument("-t", "--test", action='store_true',
help="Runs smoke tests.")
parser.add_argument("--fulltest", action='store_true',
help="Runs all pytest tests. If `pytest-xdist` installed, parallel with `--nthread`.")
# For plugins
parser.add_argument("--plugin-name", help="""\
Creates a new directory with files for writing a new plugin.
You can specify an additional argument that specifies a
template to use, for example
>>> psi4 --plugin-name mygreatcode --plugin-template mointegrals""")
choices=['ambit', 'aointegrals', 'basic', 'dfmp2', 'mointegrals', 'scf', 'sointegrals', 'wavefunction'],
help='Selects new plugin template to use.')
parser.add_argument('--plugin-compile', action='store_true', help="""\
Generates a CMake command for building a plugin against this Psi4 installation.
>>> cd <plugin_directory>
>>> `psi4 --plugin-compile`
>>> make
>>> psi4""")
# yapf: enable
# print("Environment Variables\n");
# print(" PSI_SCRATCH Directory where scratch files are written.")
# print(" Default: $TMPDIR (or /tmp/ when not set)")
# print(" This should be a local, not network, disk")
# parser.print_help()
args, unknown = parser.parse_known_args()
args = args.__dict__ # Namespace object seems silly
# Figure out pythonpath
cmake_install_prefix = os.path.normpath(os.path.dirname(os.path.abspath(__file__)) + os.path.sep + '..')
lib_dir = os.path.sep.join([cmake_install_prefix, "@CMAKE_INSTALL_LIBDIR@", "@PYMOD_INSTALL_LIBDIR@"])
if args["inplace"]:
if "CMAKE_INSTALL_LIBDIR" not in lib_dir:
raise ImportError("Cannot run inplace from an installed directory.")
import sysconfig
core_location = os.path.dirname(os.path.abspath(__file__)) + os.path.sep + "core" + sysconfig.get_config_var("EXT_SUFFIX")
if not os.path.isfile(core_location):
raise ImportError("A compiled Psi4 core{} needs to be symlinked to the {} folder".format(
sysconfig.get_config_var("EXT_SUFFIX"), os.path.dirname(__file__)))
lib_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
if ("PSIDATADIR" not in os.environ.keys()) and (not args["psidatadir"]):
data_dir = os.path.sep.join([os.path.abspath(os.path.dirname(__file__)), "share", "psi4"])
os.environ["PSIDATADIR"] = data_dir
elif "CMAKE_INSTALL_LIBDIR" in lib_dir:
raise ImportError("Psi4 was not installed correctly!")
# Replace input/output if unknown kwargs
if len(unknown) > 0:
args["input"] = unknown[0]
if len(unknown) > 1:
args["output"] = unknown[1]
if len(unknown) > 2:
raise KeyError("Too many unknown arguments: %s" % str(unknown))
# Figure out output arg
if args["output"] is None:
if args["input"] == "input.dat":
args["output"] = "output.dat"
elif args["input"].endswith(".in"):
args["output"] = args["input"][:-2] + "out"
elif args["input"].endswith(".dat"):
args["output"] = args["input"][:-3] + "out"
args["output"] = args["input"] + ".dat"
# Plugin compile line
if args['plugin_compile']:
share_cmake_dir = os.path.sep.join([cmake_install_prefix, 'share', 'cmake', 'psi4'])
plugincachealongside = os.path.isfile(share_cmake_dir + os.path.sep + 'psi4PluginCache.cmake')
if plugincachealongside:
print("""cmake -C {}/psi4PluginCache.cmake -DCMAKE_PREFIX_PATH={} .""".format(
share_cmake_dir, cmake_install_prefix))
print("""Install "psi4-dev" via `conda install psi4-dev -c psi4[/label/dev]`, then reissue command.""")
if args['psiapi_path']:
pyexe_dir = os.path.dirname("@PYTHON_EXECUTABLE@")
print("""export PATH={}:$PATH\nexport PYTHONPATH={}:$PYTHONPATH""".format(pyexe_dir, lib_dir))
# Transmit any argument psidatadir through environ
if args["psidatadir"] is not None:
data_dir = os.path.abspath(os.path.expanduser(args["psidatadir"]))
os.environ["PSIDATADIR"] = data_dir
### Actually import psi4 and apply setup ###
# Arrange for warnings to ignore everything except the message
def custom_formatwarning(msg, *args, **kwargs):
return str(msg) + '\n'
import warnings
warnings.formatwarning = custom_formatwarning
# Import installed psi4
sys.path.insert(1, lib_dir)
import psi4
if args["version"]:
# Prevents a poor option combination
if args['plugin_template'] and (not args['plugin_name']):
raise KeyError("Please specify a '--plugin-name' for your plugin template!")
if args['plugin_name']:
# Set the flag
if not args['plugin_template']:
args['plugin_template'] = 'basic'
# This call does not return.
psi4.plugin.create_plugin(args['plugin_name'], args['plugin_template'])
if args["test"]:
retcode = psi4.test('smoke')
if args["fulltest"]:
nthread = int(args["nthread"])
if nthread == 1:
extras = None
extras = ['-n', str(nthread)]
retcode = psi4.test('full', extras=extras)
if not os.path.isfile(args["input"]):
raise KeyError("The file %s does not exist." % args["input"])
args["input"] = os.path.normpath(args["input"])
# Setup outfile
if args["append"] is None:
args["append"] = False
if args["output"] != "stdout":
psi4.core.set_output_file(args["output"], args["append"])
# Set a few options
if args["prefix"] is not None:
psi4.core.set_num_threads(int(args["nthread"]), quiet=True)
psi4.core.set_memory_bytes(524288000, True)
psi4.extras._input_dir_ = os.path.dirname(os.path.abspath(args["input"]))
start_time =
# Prepare scratch for inputparser
if args["scratch"] is not None:
if not os.path.isdir(args["scratch"]):
raise Exception("Passed in scratch is not a directory (%s)." % args["scratch"])
# If this is a json call, compute and stop
if args["json"]:
with open(args["input"], 'r') as f:
json_data = json.load(f)
psi4.extras._success_flag_ = True
json_data = psi4.json_wrapper.run_json(json_data)
with open(args["input"], 'w') as f:
json.dump(json_data, f)
if args["output"] != "stdout":
# Read input
with open(args["input"]) as f:
content =
# Preprocess
if not args["skip_preprocessor"]:
# PSI_SCRATCH must be set before this call!
content = psi4.process_input(content)
# Handle Verbose
if args["verbose"]:
psi4.core.print_out('\nParsed Psithon:')
psi4.core.print_out('-' * 75)
# Handle Messy
_clean_functions = [psi4.core.clean, psi4.extras.clean_numpy_files]
if args["messy"]:
if sys.version_info >= (3, 0):
for func in _clean_functions:
for handler in atexit._exithandlers:
for func in _clean_functions:
if handler[0] == func:
# Register exit printing, failure GOTO coffee ELSE beer
atexit.register(psi4.extras.exit_printing, start_time)
# Run the program!
psi4.extras._success_flag_ = True
# Capture _any_ python error message
except Exception as exception:
import traceback
exc_type, exc_value, exc_traceback = sys.exc_info()
tb_str = "Traceback (most recent call last):\n"
tb_str += ''.join(traceback.format_tb(exc_traceback))
tb_str += '\n'
tb_str += type(exception).__name__
tb_str += ': '
tb_str += str(exception)
psi4.core.print_out("Printing out the relevant lines from the Psithon --> Python processed input file:\n")
lines = content.splitlines()
suspect_lineno = traceback.extract_tb(exc_traceback)[1].lineno - 1 # -1 for 0 indexing
first_line = max(0, suspect_lineno - 5) # Try to show five lines back...
last_line = min(len(lines), suspect_lineno + 6) # Try to show five lines forward
for line in lines[first_line:suspect_lineno]:
psi4.core.print_out(" " + line + "\n")
psi4.core.print_out("--> " + lines[suspect_lineno] + "\n")
for line in lines[suspect_lineno + 1:last_line]:
psi4.core.print_out(" " + line + "\n")
if psi4.core.get_output_file() != "stdout":
# elif '***HDF5 library version mismatched error***' in str(err):
# raise ImportError("{0}\nLikely cause: HDF5 used in compilation not prominent enough in RPATH/[DY]LD_LIBRARY_PATH".format(err))