diff --git a/pycgtool/bondset.py b/pycgtool/bondset.py
index 0ce9e97e30afc13cceaed1c04973fbd3ee2db8ee..e8184db1d5bf22263cf6821c4b99d4cc428a20bc 100644
--- a/pycgtool/bondset.py
+++ b/pycgtool/bondset.py
@@ -31,7 +31,7 @@ class Bond:
Bond lengths, angles and dihedrals are all equivalent, distinguished by the number of atoms present.
"""
- __slots__ = ["atoms", "atom_numbers", "values", "eqm", "fconst", "_func_form"]
+ __slots__ = ["atoms", "atom_numbers", "values", "eqm", "fconst", "gromacs_type_id", "_func_form"]
def __init__(self, atoms, atom_numbers=None, func_form=None):
"""
@@ -48,6 +48,7 @@ class Bond:
self.fconst = None
self._func_form = func_form
+ self.gromacs_type_id = func_form.gromacs_type_id_by_natoms(len(atoms))
def __len__(self):
return len(self.atoms)
@@ -273,10 +274,9 @@ class BondSet:
if bonds:
print("\n[ {0:s} ]".format(section_header), file=itp)
for bond in bonds:
- # Factor is usually 1, unless doing correction
line = " ".join(["{0:4d}".format(atnum + 1) for atnum in bond.atom_numbers])
eqm = math.degrees(bond.eqm) if rad2deg else bond.eqm
- line += " {0:4d} {1:12.5f}".format(1, eqm)
+ line += " {0:4d} {1:12.5f}".format(bond.gromacs_type_id, eqm)
if print_fconst:
line += " {0:12.5f}".format(bond.fconst)
if multiplicity is not None:
diff --git a/pycgtool/functionalforms.py b/pycgtool/functionalforms.py
index 987d96d87bc0105a7c64c242c070734226999f9b..7c35f78bde36af7424fe3585864767a3ab00d9f8 100644
--- a/pycgtool/functionalforms.py
+++ b/pycgtool/functionalforms.py
@@ -67,7 +67,6 @@ class FunctionalForm(object, metaclass=abc.ABCMeta):
"""
return np.nanmean(values)
- @staticmethod
@abc.abstractstaticmethod
def fconst(values, temp):
"""
@@ -78,10 +77,34 @@ class FunctionalForm(object, metaclass=abc.ABCMeta):
:param temp: Temperature of simulation
:return: Calculated force constant
"""
- pass
+ raise NotImplementedError
+
+ @abc.abstractproperty
+ def gromacs_type_ids(self):
+ """
+ Return tuple of GROMACS potential type ids when used as length, angle, dihedral.
+
+ :return tuple[int]: Tuple of GROMACS potential type ids
+ """
+ raise NotImplementedError
+
+ @classmethod
+ def gromacs_type_id_by_natoms(cls, natoms):
+ """
+ Return the GROMACS potential type id for this functional form when used with natoms.
+
+ :param int natoms:
+ :return int: GROMACS potential type id
+ """
+ tipe = cls.gromacs_type_ids[natoms - 2]
+ if tipe is None:
+ raise TypeError("The functional form {0} does not have a defined GROMACS potential type when used with {1} atoms.".format(cls.__name__, natoms))
+ return tipe
class Harmonic(FunctionalForm):
+ gromacs_type_ids = (1, 1, 1) # Consider whether to use improper (type 2) instead, it is actually harmonic
+
@staticmethod
def fconst(values, temp):
rt = 8.314 * temp / 1000.
@@ -90,6 +113,8 @@ class Harmonic(FunctionalForm):
class CosHarmonic(FunctionalForm):
+ gromacs_type_ids = (None, 2, None)
+
@staticmethod
def fconst(values, temp):
rt = 8.314 * temp / 1000.
@@ -99,18 +124,24 @@ class CosHarmonic(FunctionalForm):
class MartiniDefaultLength(FunctionalForm):
+ gromacs_type_ids = (1, None, None)
+
@staticmethod
def fconst(values, temp):
return 1250.
class MartiniDefaultAngle(FunctionalForm):
+ gromacs_type_ids = (None, 2, None)
+
@staticmethod
def fconst(values, temp):
return 25.
class MartiniDefaultDihedral(FunctionalForm):
+ gromacs_type_ids = (None, None, 1)
+
@staticmethod
def fconst(values, temp):
return 50.
diff --git a/test/data/sugar_out.itp b/test/data/sugar_out.itp
index 2a9a5b7e53c5b0f603cf84242419adf4c96d0f6a..60a9f1077eb62095205d8cb4ea761759f82c60b7 100644
--- a/test/data/sugar_out.itp
+++ b/test/data/sugar_out.itp
@@ -24,12 +24,12 @@ ALLA 1
5 6 1 0.20597 55319.39933
[ angles ]
- 1 2 3 1 77.88207 503.72544
- 2 3 4 1 116.08126 838.60326
- 3 4 5 1 111.02889 733.45020
- 4 5 6 1 83.28583 946.13165
- 5 6 1 1 143.48577 771.65933
- 6 1 2 1 99.29372 800.62783
+ 1 2 3 2 77.88207 503.72544
+ 2 3 4 2 116.08126 838.60326
+ 3 4 5 2 111.02889 733.45020
+ 4 5 6 2 83.28583 946.13165
+ 5 6 1 2 143.48577 771.65933
+ 6 1 2 2 99.29372 800.62783
[ dihedrals ]
1 2 3 4 1 -82.85912 253.69305 1
diff --git a/test/test_bondset.py b/test/test_bondset.py
index 7394917c000f548990174ab3c0bfefe40b110a6c..66eb451afebc047b20e32fb79dabe8058757bfe9 100644
--- a/test/test_bondset.py
+++ b/test/test_bondset.py
@@ -24,26 +24,26 @@ class DummyOptions:
class BondSetTest(unittest.TestCase):
- # Columns are: eqm value, standard fc, defaults fc, mixed fc
+ # Columns are: eqm value, standard fc, MARTINI defaults fc
invert_test_ref_data = [
- ( 0.220474419132, 72658.18163, 1250, 1520530.416),
- ( 0.221844516963, 64300.01188, 1250, 1328761.015),
- ( 0.216313356504, 67934.93368, 1250, 1474281.672),
- ( 0.253166204438, 19545.27388, 1250, 311446.690),
- ( 0.205958461836, 55359.06367, 1250, 1322605.992),
- ( 0.180550961226, 139643.66601, 1250, 4334538.941),
- ( 1.359314249473, 503.24211, 25, 481.527),
- ( 2.026002746003, 837.76904, 25, 676.511),
- ( 1.937848056214, 732.87969, 25, 639.007),
- ( 1.453592079716, 945.32633, 25, 933.199),
- ( 2.504189933347, 771.63691, 25, 273.207),
- ( 1.733002945619, 799.82825, 25, 779.747),
- (-1.446051810383, 253.75691, 50, 1250),
- ( 1.067436470329, 125.04591, 50, 1250),
- (-0.373528903861, 135.50927, 50, 1250),
- ( 0.927837103158, 51.13975, 50, 1250),
- (-1.685096988856, 59.38162, 50, 1250),
- ( 1.315458354592, 279.80889, 50, 1250)
+ ( 0.220474419132, 72658.18163, 1250),
+ ( 0.221844516963, 64300.01188, 1250),
+ ( 0.216313356504, 67934.93368, 1250),
+ ( 0.253166204438, 19545.27388, 1250),
+ ( 0.205958461836, 55359.06367, 1250),
+ ( 0.180550961226, 139643.66601, 1250),
+ ( 1.359314249473, 503.24211, 25),
+ ( 2.026002746003, 837.76904, 25),
+ ( 1.937848056214, 732.87969, 25),
+ ( 1.453592079716, 945.32633, 25),
+ ( 2.504189933347, 771.63691, 25),
+ ( 1.733002945619, 799.82825, 25),
+ (-1.446051810383, 253.75691, 50),
+ ( 1.067436470329, 125.04591, 50),
+ (-0.373528903861, 135.50927, 50),
+ ( 0.927837103158, 51.13975, 50),
+ (-1.685096988856, 59.38162, 50),
+ ( 1.315458354592, 279.80889, 50)
]
def test_bondset_create(self):
@@ -119,11 +119,11 @@ class BondSetTest(unittest.TestCase):
measure.boltzmann_invert()
self.support_check_mean_fc(measure["ALLA"], 2)
- def test_bondset_boltzmann_invert_func_forms(self):
+ def test_bondset_boltzmann_invert_manual_default_fc(self):
class FuncFormOptions(DummyOptions):
- length_form = "CosHarmonic"
- angle_form = "Harmonic"
- dihedral_form = "MartiniDefaultLength"
+ length_form = "MartiniDefaultLength"
+ angle_form = "MartiniDefaultAngle"
+ dihedral_form = "MartiniDefaultDihedral"
measure = BondSet("test/data/sugar.bnd", FuncFormOptions)
frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc")
@@ -135,7 +135,7 @@ class BondSetTest(unittest.TestCase):
measure.apply(cgframe)
measure.boltzmann_invert()
- self.support_check_mean_fc(measure["ALLA"], 3)
+ self.support_check_mean_fc(measure["ALLA"], 2)
@unittest.skipIf(not mdtraj_present, "MDTRAJ or Scipy not present")
def test_bondset_boltzmann_invert_mdtraj(self):
diff --git a/test/test_functionalforms.py b/test/test_functionalforms.py
index 78a4464d706c19c3fea4210207b21e1ddc6b0a3c..b68da2891d34d8139ea538500b804fc1da3a0f7a 100644
--- a/test/test_functionalforms.py
+++ b/test/test_functionalforms.py
@@ -13,6 +13,8 @@ class FunctionalFormTest(unittest.TestCase):
def test_functional_form_new(self):
class TestFunc(FunctionalForm):
+ gromacs_type_ids = (None, None, None)
+
@staticmethod
def eqm(values, temp):
return "TestResultEqm"