From ab22ad423e20c207074d5c5e274f8f7fd7247c6c Mon Sep 17 00:00:00 2001 From: James Graham <J.A.Graham@soton.ac.uk> Date: Fri, 16 Dec 2016 11:28:36 +0000 Subject: [PATCH] Remove empirical_scale and factor_2 from options They were useful during testing, but are now unnecessary --- doc/tutorial_files/md.mdp | 1 - pycgtool.py | 2 -- pycgtool/bondset.py | 19 ++----------------- test/test_pycgtool.py | 2 +- 4 files changed, 3 insertions(+), 21 deletions(-) diff --git a/doc/tutorial_files/md.mdp b/doc/tutorial_files/md.mdp index 04fc9ef..4d82b1f 100644 --- a/doc/tutorial_files/md.mdp +++ b/doc/tutorial_files/md.mdp @@ -29,7 +29,6 @@ nstxout-compressed = 1000 compressed-x-precision = 100 compressed-x-grps = System energygrps = System -imd-group = Other ; NEIGHBOURLIST and MARTINI ; To achieve faster simulations in combination with the Verlet-neighborlist diff --git a/pycgtool.py b/pycgtool.py index 4de6f40..6082e27 100755 --- a/pycgtool.py +++ b/pycgtool.py @@ -39,8 +39,6 @@ if __name__ == "__main__": ("default_fc", False), ("generate_angles", True), ("generate_dihedrals", False), - ("empirical_corr", False), - ("factor_two", 1), ("length_form", "harmonic"), ("angle_form", "cosharmonic"), ("dihedral_form", "harmonic") diff --git a/pycgtool/bondset.py b/pycgtool/bondset.py index 9dce2ac..def598f 100644 --- a/pycgtool/bondset.py +++ b/pycgtool/bondset.py @@ -105,14 +105,6 @@ class BondSet: self._fconst_constr_threshold = options.constr_threshold - self._empirical_correction_factor = 1. - try: - self._empirical_correction = options.empirical_corr - if self._empirical_correction: - self._empirical_correction_factor = 1.05 - except AttributeError: - self._empirical_correction = False - try: self._temperature = options.temperature except AttributeError: @@ -123,11 +115,6 @@ class BondSet: except AttributeError: self._default_fc = False - try: - self._factor_two = options.factor_two - except AttributeError: - self._factor_two = 1 - functional_forms = FunctionalForms() self._functional_forms = {} try: @@ -290,12 +277,10 @@ class BondSet: print("\n[ {0:s} ]".format(section_header), file=itp) for bond in bonds: # Factor is usually 1, unless doing correction - eqm = bond.eqm * self._empirical_correction_factor - fconst = bond.fconst * self._empirical_correction_factor line = " ".join(["{0:4d}".format(atnum + 1) for atnum in bond.atom_numbers]) - line += " {0:4d} {1:12.5f}".format(1, eqm) + line += " {0:4d} {1:12.5f}".format(1, bond.eqm) if print_fconst: - line += " {0:12.5f}".format(fconst) + line += " {0:12.5f}".format(bond.fconst) if multiplicity is not None: line += " {0:4d}".format(multiplicity) print(line, file=itp) diff --git a/test/test_pycgtool.py b/test/test_pycgtool.py index 9667425..ab03b97 100644 --- a/test/test_pycgtool.py +++ b/test/test_pycgtool.py @@ -37,7 +37,7 @@ class PycgtoolTest(unittest.TestCase): ("map_center", "geom"), ("constr_threshold", 100000), ("dump_measurements", False), - ("dump_n_values", 100000), + ("dump_n_values", 10000), ("output_forcefield", False), ("temperature", 310), ("default_fc", False), -- GitLab