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Commit ab22ad42 authored by James Graham's avatar James Graham
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Remove empirical_scale and factor_2 from options

They were useful during testing, but are now unnecessary
parent fad8ceb0
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...@@ -29,7 +29,6 @@ nstxout-compressed = 1000 ...@@ -29,7 +29,6 @@ nstxout-compressed = 1000
compressed-x-precision = 100 compressed-x-precision = 100
compressed-x-grps = System compressed-x-grps = System
energygrps = System energygrps = System
imd-group = Other
; NEIGHBOURLIST and MARTINI ; NEIGHBOURLIST and MARTINI
; To achieve faster simulations in combination with the Verlet-neighborlist ; To achieve faster simulations in combination with the Verlet-neighborlist
......
...@@ -39,8 +39,6 @@ if __name__ == "__main__": ...@@ -39,8 +39,6 @@ if __name__ == "__main__":
("default_fc", False), ("default_fc", False),
("generate_angles", True), ("generate_angles", True),
("generate_dihedrals", False), ("generate_dihedrals", False),
("empirical_corr", False),
("factor_two", 1),
("length_form", "harmonic"), ("length_form", "harmonic"),
("angle_form", "cosharmonic"), ("angle_form", "cosharmonic"),
("dihedral_form", "harmonic") ("dihedral_form", "harmonic")
......
...@@ -105,14 +105,6 @@ class BondSet: ...@@ -105,14 +105,6 @@ class BondSet:
self._fconst_constr_threshold = options.constr_threshold 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: try:
self._temperature = options.temperature self._temperature = options.temperature
except AttributeError: except AttributeError:
...@@ -123,11 +115,6 @@ class BondSet: ...@@ -123,11 +115,6 @@ class BondSet:
except AttributeError: except AttributeError:
self._default_fc = False self._default_fc = False
try:
self._factor_two = options.factor_two
except AttributeError:
self._factor_two = 1
functional_forms = FunctionalForms() functional_forms = FunctionalForms()
self._functional_forms = {} self._functional_forms = {}
try: try:
...@@ -290,12 +277,10 @@ class BondSet: ...@@ -290,12 +277,10 @@ class BondSet:
print("\n[ {0:s} ]".format(section_header), file=itp) print("\n[ {0:s} ]".format(section_header), file=itp)
for bond in bonds: for bond in bonds:
# Factor is usually 1, unless doing correction # 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 = " ".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: if print_fconst:
line += " {0:12.5f}".format(fconst) line += " {0:12.5f}".format(bond.fconst)
if multiplicity is not None: if multiplicity is not None:
line += " {0:4d}".format(multiplicity) line += " {0:4d}".format(multiplicity)
print(line, file=itp) print(line, file=itp)
......
...@@ -37,7 +37,7 @@ class PycgtoolTest(unittest.TestCase): ...@@ -37,7 +37,7 @@ class PycgtoolTest(unittest.TestCase):
("map_center", "geom"), ("map_center", "geom"),
("constr_threshold", 100000), ("constr_threshold", 100000),
("dump_measurements", False), ("dump_measurements", False),
("dump_n_values", 100000), ("dump_n_values", 10000),
("output_forcefield", False), ("output_forcefield", False),
("temperature", 310), ("temperature", 310),
("default_fc", False), ("default_fc", False),
......
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