Merge pull request #23 from libefp2/pylibefp2

Bringing pylibefp functionality in sync with the master libefp version. Long overdue.

Author: slipchenko

.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/__pycache__/__init__.cpython-312.pyc

@@ -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/__pycache__/exceptions.cpython-312.pyc

@@ -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