Merge pull request #1810 from glotzerlab/enhancement/md-pair-gaussian…

…-value-check Enhancement/md pair gaussian value check
glotzerlab · Jun 24, 2024 · 9f19af0 · 9f19af0
2 parents fc5a5e0 + 298aafc
commit 9f19af0
Show file tree

Hide file tree

Showing 3 changed files with 18 additions and 7 deletions.
diff --git a/hoomd/md/pair/pair.py b/hoomd/md/pair/pair.py
@@ -12,7 +12,7 @@
 from hoomd.data.parameterdicts import ParameterDict, TypeParameterDict
 from hoomd.data.typeparam import TypeParameter
 import numpy as np
-from hoomd.data.typeconverter import OnlyFrom, nonnegative_real
+from hoomd.data.typeconverter import OnlyFrom, nonnegative_real, positive_real
 
 
 class Pair(force.Force):
@@ -257,7 +257,7 @@ class Gaussian(Pair):
 
         * ``epsilon`` (`float`, **required**) - energy parameter
           :math:`\varepsilon` :math:`[\mathrm{energy}]`
-        * ``sigma`` (`float`, **required**) - particle size :math:`\sigma`
+        * ``sigma`` (`float`, **required**) - particle size :math:`\sigma > 0`
           :math:`[\mathrm{length}]`
 
         Type: `TypeParameter` [`tuple` [``particle_type``, ``particle_type``],
@@ -275,7 +275,7 @@ def __init__(self, nlist, default_r_cut=None, default_r_on=0., mode='none'):
         super().__init__(nlist, default_r_cut, default_r_on, mode)
         params = TypeParameter(
             'params', 'particle_types',
-            TypeParameterDict(epsilon=float, sigma=float, len_keys=2))
+            TypeParameterDict(epsilon=float, sigma=positive_real, len_keys=2))
         self._add_typeparam(params)
 
 
@@ -311,7 +311,7 @@ class ExpandedGaussian(Pair):
         * ``epsilon`` (`float`, **required**) - energy parameter
           :math:`\varepsilon` :math:`[\mathrm{energy}]`
         * ``sigma`` (`float`, **required**) - particle size
-          :math:`\sigma` :math:`[\mathrm{length}]`
+          :math:`\sigma > 0` :math:`[\mathrm{length}]`
         * ``delta`` (`float`, **required**) - shift distance
           :math:`\delta` :math:`[\mathrm{length}]`
 
@@ -331,7 +331,7 @@ def __init__(self, nlist, default_r_cut=None, default_r_on=0., mode='none'):
         params = TypeParameter(
             'params', 'particle_types',
             TypeParameterDict(epsilon=float,
-                              sigma=float,
+                              sigma=positive_real,
                               delta=float,
                               len_keys=2))
         self._add_typeparam(params)
@@ -1844,7 +1844,7 @@ class LJGauss(Pair):
         * ``epsilon`` (`float`, **required**) -
           energy parameter :math:`\varepsilon` :math:`[\mathrm{energy}]`
         * ``sigma`` (`float`, **required**) -
-          Gaussian width :math:`\sigma` :math:`[\mathrm{length}]`
+          Gaussian width :math:`\sigma > 0` :math:`[\mathrm{length}]`
         * ``r0`` (`float`, **required**) -
           Gaussian center :math:`r_0` :math:`[\mathrm{length}]`
 
@@ -1868,5 +1868,8 @@ def __init__(self,
         super().__init__(nlist, default_r_cut, default_r_on, mode)
         params = TypeParameter(
             'params', 'particle_types',
-            TypeParameterDict(epsilon=float, sigma=float, r0=float, len_keys=2))
+            TypeParameterDict(epsilon=float,
+                              sigma=positive_real,
+                              r0=float,
+                              len_keys=2))
         self._add_typeparam(params)
diff --git a/hoomd/md/pytest/test_potential.py b/hoomd/md/pytest/test_potential.py
@@ -182,6 +182,7 @@ def _invalid_params():
 
     gauss_valid_dict = {'sigma': 0.05, 'epsilon': 0.05}
     gauss_invalid_dicts = _make_invalid_param_dict(gauss_valid_dict)
+    gauss_invalid_dicts.append({'sigma': 0, 'epsilon': 0.05})
     invalid_params_list.extend(
         _make_invalid_params(gauss_invalid_dicts, md.pair.Gaussian, {}))
 
@@ -192,6 +193,11 @@ def _invalid_params():
     }
     expanded_gaussian_invalid_dicts = _make_invalid_param_dict(
         expanded_gaussian_valid_dict)
+    expanded_gaussian_invalid_dicts.append({
+        'sigma': 0,
+        'epsilon': 0.05,
+        'delta': 0.1
+    })
     invalid_params_list.extend(
         _make_invalid_params(expanded_gaussian_invalid_dicts,
                              md.pair.ExpandedGaussian, {}))
@@ -316,6 +322,7 @@ def _invalid_params():
 
     ljgauss_valid_dict = {'r0': 1.8, 'epsilon': 2.0, 'sigma': 0.02}
     ljgauss_invalid_dicts = _make_invalid_param_dict(ljgauss_valid_dict)
+    ljgauss_invalid_dicts.append({'r0': 1.8, 'epsilon': 0.2, 'sigma': 0})
     invalid_params_list.extend(
         _make_invalid_params(ljgauss_invalid_dicts, hoomd.md.pair.LJGauss, {}))
     table_valid_dict = {

diff --git a/sphinx-doc/credits.rst b/sphinx-doc/credits.rst
@@ -65,6 +65,7 @@ The following people have contributed to HOOMD-blue:
 * Jenny Fothergill, Boise State University
 * Jens Glaser, Oak Ridge National Laboratory
 * Joseph Berleant, University of Michigan
+* Joseph Burkhart, University of Michigan
 * Joshua A. Anderson, University of Michigan
 * Kelly Wang, University of Michigan
 * Kevin Daly, Princeton University