Pylibefp2

.gitignore

@@ -24,7 +24,11 @@
 /include/
 tags
 build*/
-/installed/
+/install*/
 /cmake-build-debug/
-compilation.log
-
+comp*.log
+/lib
+.DS_Store
+__pycache__/
+*.pyc
+*.pyo

cpp.sh

@@ -0,0 +1,9 @@
+rm -rf build
+rm -rf installed
+
+cmake -S . -B build \
+    -D CMAKE_INSTALL_PREFIX=$LIBEFP_DIR/installed \
+    -D BUILD_SHARED_LIBS=ON \
+    -D LIBEFP_ENABLE_OPENMP=ON
+
+cmake --build build --target install

efpmd/src/main.c

@@ -445,7 +445,7 @@ static void state_init(struct state *state, const struct cfg *cfg, const struct
 	state->energy = 0;
 	state->grad = xcalloc(sys->n_frags * 6 + sys->n_charges * 3, sizeof(double));
 	state->ff = NULL;
-    	state->torch = NULL;
+    state->torch = NULL;
 	state->torch_grad = NULL;
 
 	if (cfg_get_bool(cfg, "enable_ff")) {
@@ -472,6 +472,7 @@ static void state_init(struct state *state, const struct cfg *cfg, const struct
     // initiate torch state
 #ifdef TORCH_SWITCH
     if (cfg_get_bool(cfg, "enable_torch")) {
+        check_fail(efp_get_frag_count(state->efp, &nfrag));
         if (cfg_get_int(cfg, "special_fragment") < 0 || cfg_get_int(cfg, "special_fragment") > nfrag-1)
             error("do not know for which fragment to compute torch: set special_fragment");
 

lib/pylibefp/__init__.py

@@ -0,0 +1,26 @@
+#
+# @BEGIN LICENSE
+#
+#   pylibefp/__init__.py:
+#
+#   Copyright (c) 2017-2019 The Psi4 Developers
+#
+#   All rights reserved. Use of this source code is governed by a
+#   BSD-style license that can be found in the LICENSE file.
+#
+# @END LICENSE
+#
+
+import os
+pylibefp_module_loc = os.path.dirname(os.path.abspath(__file__))
+
+# Init core
+from . import core
+
+# Load driver and version paraphernalia
+from .wrapper import from_dict, to_dict
+from .exceptions import EFPException, Fatal, NoMemory, FileNotFound, EFPSyntaxError, UnknownFragment, PolNotConverged, PyEFPSyntaxError
+__version__ = "2.0.0"
+
+# A few extraneous functions
+from .extras import test

lib/pylibefp/exceptions.py

@@ -0,0 +1,68 @@
+#
+# @BEGIN LICENSE
+#
+#   pylibefp/wrapper/exceptions.py:
+#
+#   Copyright (c) 2017-2019 The Psi4 Developers
+#
+#   All rights reserved. Use of this source code is governed by a
+#   BSD-style license that can be found in the LICENSE file.
+#
+# @END LICENSE
+#
+"""Module with non-generic exceptions classes."""
+from . import extras
+
+
+class EFPException(Exception):
+    """Error class for pylibefp."""
+    extras._success_flag_ = False
+
+
+class Fatal(EFPException):
+    """Fatal error has occurred."""
+    def __init__(self, msg):
+        EFPException.__init__(self, msg)
+        self.message = r"""\nEFPException: Fatal error has occurred. {}\n\n""".format(repr(msg))
+
+
+class NoMemory(EFPException):
+    """Insufficient memory."""
+    def __init__(self, msg):
+        EFPException.__init__(self, msg)
+        self.message = r"""\nEFPException: Insufficient memory. {}\n\n""".format(repr(msg))
+
+
+class FileNotFound(EFPException):
+    """File not found."""
+    def __init__(self, msg):
+        EFPException.__init__(self, msg)
+        self.message = r"""\nEFPException: File not found. {}\n\n""".format(repr(msg))
+
+
+class EFPSyntaxError(EFPException):
+    """Syntax error."""
+    def __init__(self, msg):
+        EFPException.__init__(self, msg)
+        self.message = r"""\nEFPException: Libefp syntax error. {}\n\n""".format(repr(msg))
+
+
+class UnknownFragment(EFPException):
+    """Unknown EFP fragment."""
+    def __init__(self, msg):
+        EFPException.__init__(self, msg)
+        self.message = r"""\nEFPException: Unknown EFP fragment. {}\n\n""".format(repr(msg))
+
+
+class PolNotConverged(EFPException):
+    """Polarization SCF procedure did not converge."""
+    def __init__(self, msg):
+        EFPException.__init__(self, msg)
+        self.message = r"""\nEFPException: Polarization SCF procedure did not converge. {}\n\n""".format(repr(msg))
+
+
+class PyEFPSyntaxError(EFPException):
+    """Syntax error."""
+    def __init__(self, msg):
+        EFPException.__init__(self, msg)
+        self.message = r"""\nEFPException: Pylibefp syntax error. {}\n\n""".format(repr(msg))

lib/pylibefp/extras.py

@@ -0,0 +1,64 @@
+#
+# @BEGIN LICENSE
+#
+#   pylibefp/extras.py:
+#
+#   Copyright (c) 2017-2019 The Psi4 Developers
+#
+#   All rights reserved. Use of this source code is governed by a
+#   BSD-style license that can be found in the LICENSE file.
+#
+# @END LICENSE
+#
+
+import os
+
+_success_flag_ = False
+
+###   # Working directory
+###   _input_dir_ = os.getcwd()
+###
+###   def get_input_directory():
+###       return _input_dir_
+
+
+# Testing
+def test(extent='full', extras=None):
+    """Runs a test suite through pytest.
+
+    Parameters
+    ----------
+    extent : {'smoke', 'quick', 'full', 'long'}
+        All choices are defined, but choices may be redundant in some projects.
+        _smoke_ will be minimal "is-working?" test(s).
+        _quick_ will be as much coverage as can be got quickly, approx. 1/3 tests.
+        _full_ will be the whole test suite, less some exceedingly long outliers.
+        _long_ will be the whole test suite.
+    extras : list
+        Additional arguments to pass to `pytest`.
+
+    Returns
+    -------
+    int
+        Return code from `pytest.main()`. 0 for pass, 1 for fail.
+
+    """
+    try:
+        import pytest
+    except ImportError:
+        raise RuntimeError('Testing module `pytest` is not installed. Run `conda install pytest`')
+    abs_test_dir = os.path.sep.join([os.path.abspath(os.path.dirname(__file__)), "tests"])
+
+    command = ['-rws', '-v']
+    if extent.lower() in ['smoke', 'quick']:
+        command.extend(['-m', 'quick'])
+    elif extent.lower() == 'full':
+        command.extend(['-m', 'not long'])
+    elif extent.lower() == 'long':
+        pass
+    if extras is not None:
+        command.extend(extras)
+    command.extend(['--capture=sys', abs_test_dir])
+
+    retcode = pytest.main(command)
+    return retcode

lib/pylibefp/tests/addons.py

@@ -0,0 +1,19 @@
+import pytest
+
+from qcelemental.util import which_import, parse_version
+
+
+def is_psi4_new_enough(version_feature_introduced):
+    if which_import('psi4') is None:
+        return False
+    import psi4
+    return parse_version(psi4.__version__) >= parse_version(version_feature_introduced)
+
+
+using_psi4 = pytest.mark.skipif(
+    which_import('psi4', return_bool=True) is False,
+    reason='Not detecting package psi4. Install package if necessary and and to envvar PYTHONPATH')
+
+using_psi4_efpmints = pytest.mark.skipif(
+    is_psi4_new_enough("1.2a1.dev507") is False,
+    reason="Psi4 does not include EFP integrals in mints. Update to development head")

lib/pylibefp/tests/conftest.py

@@ -0,0 +1,15 @@
+import pytest
+
+
+@pytest.fixture(scope="session", autouse=True)
+def set_up_overall(request):
+    pass
+
+
+@pytest.fixture(scope="function", autouse=True)
+def set_up():
+    pass
+
+
+def tear_down():
+    pass

lib/pylibefp/tests/systems.py

@@ -0,0 +1,147 @@
+import pylibefp
+#from utils import *
+
+b2a = 0.529177
+a2b = 1.0 / b2a
+
+
+def system_1():
+    sys = pylibefp.core.efp()
+
+    frags = ['h2o_l', 'nh3_l']  # specifying LIBRARY with _l for variety
+    sys.add_potential(frags)
+    sys.add_fragment(frags)
+    sys.set_frag_coordinates(0, 'xyzabc', [0.0 * a2b, 0.0 * a2b, 0.0 * a2b, 1.0, 2.0, 3.0])  # yapf: disable
+    sys.set_frag_coordinates(1, 'xyzabc', [5.0 * a2b, 0.0 * a2b, 0.0 * a2b, 5.0, 2.0, 8.0])  # yapf: disable
+
+    sys.prepare()
+    return sys
+
+
+def system_2():
+    sys = pylibefp.core.efp()
+
+    frags = ['h2o_l', 'nh3_l', 'h2o_l', 'h2o_l', 'nh3_l']
+    sys.add_potential(frags)
+    sys.add_fragment(frags)
+    sys.set_frag_coordinates(0, 'xyzabc', [-1.0 * a2b,   3.7 * a2b,   0.4 * a2b,  -1.3,   0.0,   7.0])  # yapf: disable
+    sys.set_frag_coordinates(1, 'xyzabc', [ 0.4 * a2b,  -0.9 * a2b,  -0.7 * a2b,   4.0,   1.6,  -2.3])  # yapf: disable
+    sys.set_frag_coordinates(2, 'xyzabc', [ 1.7 * a2b,   2.0 * a2b,   3.3 * a2b,  -1.2,  -2.0,   6.2])  # yapf: disable
+    sys.set_frag_coordinates(3, 'xyzabc', [ 0.0 * a2b,   3.9 * a2b,  -3.4 * a2b,   1.3,   5.2,  -3.0])  # yapf: disable
+    sys.set_frag_coordinates(4, 'xyzabc', [-3.5 * a2b,   0.0 * a2b,  -0.7 * a2b,   0.0,  -2.7,   2.7])  # yapf: disable
+
+    sys.prepare()
+    return sys
+
+
+def system_3():
+    sys = pylibefp.core.efp()
+
+    frags = ['h2o_l', 'nh3_l', 'nh3_l', 'nh3_l', 'ch3oh_l', 'h2o_l', 'h2o_l', 'ch3oh_l', 'h2o_l']
+    sys.add_potential(frags)
+    sys.add_fragment(frags)
+    sys.set_frag_coordinates(
+        0, 'points', [i * a2b for i in [-3.394, -1.900, -3.700, -3.524, -1.089, -3.147, -2.544, -2.340, -3.445]])
+    sys.set_frag_coordinates(1, 'points',
+                             [i * a2b for i in [-5.515, 1.083, 0.968, -5.161, 0.130, 0.813, -4.833, 1.766, 0.609]])
+    sys.set_frag_coordinates(2, 'points',
+                             [i * a2b for i in [1.848, 0.114, 0.130, 1.966, 0.674, -0.726, 0.909, 0.273, 0.517]])
+    sys.set_frag_coordinates(3, 'points',
+                             [i * a2b for i in [-1.111, -0.084, -4.017, -1.941, 0.488, -3.813, -0.292, 0.525, -4.138]])
+    sys.set_frag_coordinates(4, 'points',
+                             [i * a2b for i in [-2.056, 0.767, -0.301, -2.999, -0.274, -0.551, -1.201, 0.360, 0.258]])
+    sys.set_frag_coordinates(5, 'points',
+                             [i * a2b for i in [-0.126, -2.228, -0.815, 0.310, -2.476, 0.037, 0.053, -1.277, -1.011]])
+    sys.set_frag_coordinates(6, 'points',
+                             [i * a2b for i in [-1.850, 1.697, 3.172, -1.050, 1.592, 2.599, -2.666, 1.643, 2.614]])
+    sys.set_frag_coordinates(7, 'points',
+                             [i * a2b for i in [1.275, -2.447, -4.673, 0.709, -3.191, -3.592, 2.213, -1.978, -4.343]])
+    sys.set_frag_coordinates(
+        8, 'points', [i * a2b for i in [-5.773, -1.738, -0.926, -5.017, -1.960, -1.522, -5.469, -1.766, 0.014]])
+
+    sys.prepare()
+    return sys
+
+
+def system_4():
+    sys = pylibefp.core.efp()
+
+    frags = ['acetone_l', 'c2h5oh_l', 'c6h6_l', 'ccl4_l', 'ch3oh_l', 'ch4_l', 'cl2_l', 'dcm_l', 'dmso_l', 'h2_l', 'h2o_l', 'nh3_l']
+    sys.add_potential(frags)
+    sys.add_fragment(frags)
+    sys.set_frag_coordinates(0, 'xyzabc', [   0.0 * a2b,   0.0 * a2b,   0.0 * a2b,   0.0,   0.2,   0.3])  # yapf: disable
+    sys.set_frag_coordinates(1, 'xyzabc', [   7.0 * a2b,   0.0 * a2b,   0.0 * a2b,   0.0,   2.0,   3.7])  # yapf: disable
+    sys.set_frag_coordinates(2, 'xyzabc', [  14.0 * a2b,   0.0 * a2b,   0.0 * a2b,   3.1,   0.8,   2.0])  # yapf: disable
+    sys.set_frag_coordinates(3, 'xyzabc', [  21.0 * a2b,   0.0 * a2b,   0.0 * a2b,   0.0,   8.0,   0.0])  # yapf: disable
+    sys.set_frag_coordinates(4, 'xyzabc', [   0.0 * a2b,   6.0 * a2b,   0.0 * a2b,   0.7,   2.0,   1.0])  # yapf: disable
+    sys.set_frag_coordinates(5, 'xyzabc', [   7.0 * a2b,   6.0 * a2b,   0.0 * a2b,   0.6,   0.0,   4.7])  # yapf: disable
+    sys.set_frag_coordinates(6, 'xyzabc', [  14.0 * a2b,   6.0 * a2b,   0.0 * a2b,   0.0,   0.0,   0.3])  # yapf: disable
+    sys.set_frag_coordinates(7, 'xyzabc', [  21.0 * a2b,   6.0 * a2b,   0.0 * a2b,   0.0,   0.4,   0.3])  # yapf: disable
+    sys.set_frag_coordinates(8, 'xyzabc', [   0.0 * a2b,  12.0 * a2b,   0.0 * a2b,   0.8,   0.0,   0.0])  # yapf: disable
+    sys.set_frag_coordinates(9, 'xyzabc', [   7.0 * a2b,  12.0 * a2b,   0.0 * a2b,   8.0,   0.7,   0.8])  # yapf: disable
+    sys.set_frag_coordinates(10, 'xyzabc', [ 14.0 * a2b,  12.0 * a2b,   0.0 * a2b,   0.0,   0.0,   0.0])  # yapf: disable
+    sys.set_frag_coordinates(11, 'xyzabc', [ 21.0 * a2b,  12.0 * a2b,   0.0 * a2b,   0.0,   2.0,   0.0])  # yapf: disable
+
+    sys.prepare()
+    return sys
+
+
+def system_5():
+    sys = pylibefp.core.efp()
+
+    frags = ['h2o_l', 'nh3_l']
+    sys.add_potential(frags)
+    sys.add_fragment(frags)
+    sys.set_frag_coordinates(0, 'xyzabc', [   0.0 * a2b,   0.0 * a2b,   0.0 * a2b,   3.0,   0.0,   7.0])  # yapf: disable
+    sys.set_frag_coordinates(1, 'xyzabc', [  18.0 * a2b,  18.0 * a2b,  18.0 * a2b,   5.0,   4.0,   6.0])  # yapf: disable
+
+    sys.prepare()
+    return sys
+
+
+def system_6():
+    sys = pylibefp.core.efp()
+
+    frags = ['h2o_l', 'ch3oh_l', 'h2o_l', 'ch3oh_l', 'nh3_l']
+    sys.add_potential(frags)
+    sys.add_fragment(frags)
+    sys.set_frag_coordinates(0, 'xyzabc', [   0.0 * a2b,   0.0 * a2b,   0.0 * a2b,   0.0,   0.0,   0.0])  # yapf: disable
+    sys.set_frag_coordinates(1, 'xyzabc', [  19.0 * a2b,   0.0 * a2b,   0.0 * a2b,   0.0,   0.0,   0.0])  # yapf: disable
+    sys.set_frag_coordinates(2, 'xyzabc', [   0.0 * a2b,  19.0 * a2b,   0.0 * a2b,   0.0,   0.0,   0.0])  # yapf: disable
+    sys.set_frag_coordinates(3, 'xyzabc', [   0.0 * a2b,   0.0 * a2b,  19.0 * a2b,   0.0,   0.0,   0.0])  # yapf: disable
+    sys.set_frag_coordinates(4, 'xyzabc', [  18.0 * a2b,  18.0 * a2b,  18.0 * a2b,   0.0,   0.0,   0.0])  # yapf: disable
+
+    sys.prepare()
+    return sys
+
+
+def system_qm1():
+    sys = pylibefp.core.efp()
+
+    frags = ['h2o_l', 'c6h6_l', 'nh3_l']
+    sys.add_potential(frags)
+    sys.add_fragment(frags)
+    sys.set_frag_coordinates(0, 'xyzabc', [  -1.6 * a2b,   4.7 * a2b,   1.4 * a2b,  -1.3,   0.1,   7.0])  # yapf: disable
+    sys.set_frag_coordinates(1, 'xyzabc', [   0.4 * a2b,  -0.9 * a2b,  -0.7 * a2b,   2.3,   1.6,  -2.3])  # yapf: disable
+    sys.set_frag_coordinates(2, 'xyzabc', [  -3.5 * a2b,  -2.0 * a2b,  -0.7 * a2b,   0.0,   2.2,   2.7])  # yapf: disable
+
+    sys.prepare()
+    return sys
+
+
+def system_qm2():
+    sys = pylibefp.core.efp()
+
+    frags = ['ch3oh_l', 'dmso_l', 'dmso_l', 'acetone_l', 'dcm_l', 'acetone_l', 'acetone_l']
+    sys.add_potential(frags)
+    sys.add_fragment(frags)
+    sys.set_frag_coordinates(0, 'xyzabc', [   0.0 * a2b,  -1.0 * a2b,   0.0 * a2b,   0.0,   1.1,   2.0])  # yapf: disable
+    sys.set_frag_coordinates(1, 'xyzabc', [  -5.0 * a2b,  12.0 * a2b,   0.0 * a2b,   3.0,   0.2,   5.0])  # yapf: disable
+    sys.set_frag_coordinates(2, 'xyzabc', [   0.0 * a2b,  -3.0 * a2b,   5.0 * a2b,   6.0,   2.3,   8.0])  # yapf: disable
+    sys.set_frag_coordinates(3, 'xyzabc', [  -5.0 * a2b,  -4.0 * a2b,  -5.0 * a2b,   9.0,   0.4,   1.0])  # yapf: disable
+    sys.set_frag_coordinates(4, 'xyzabc', [  -9.0 * a2b,  -5.0 * a2b,   1.0 * a2b,   2.0,   1.5,   4.0])  # yapf: disable
+    sys.set_frag_coordinates(5, 'xyzabc', [   7.0 * a2b,  -2.0 * a2b,  11.0 * a2b,   5.0,   0.6,   7.0])  # yapf: disable
+    sys.set_frag_coordinates(6, 'xyzabc', [  -9.0 * a2b,  -7.0 * a2b,  -9.0 * a2b,   8.0,   2.7,   0.0])  # yapf: disable
+
+    sys.prepare()
+    return sys