Fixes bug in effective mass calculation (#98)

* Fixed broken links

* Added description to conda recipe

* Buf fix

README.md

@@ -31,7 +31,7 @@ different states and to identify pathways connecting them.
 
 CVPack is a Python package that provides pre-defined CVs for the powerful molecular dynamics engine
 [OpenMM]. All these CVs are subclasses of OpenMM's [Force] class and, as such, can be directly added
-to a [CustomCVForce] or used to define a [BiasVariable] for [Metadynamics], for instance.
+to a [CustomCVForce] or used to define a [BiasVariable] for [Metadynamics].
 
 Collective Variables
 --------------------
@@ -98,17 +98,17 @@ Copyright
 Copyright (c) 2023-2024 [C. Abreu](https://github.com/craabreu) & [Redesign Science](https://www.redesignscience.com)
 
 
-Acknowledgements
-----------------
+Acknowledgments
+---------------
 
 Initial project based on the [CMS Cookiecutter] version 1.1.
 
-[BiasVariable]:       https://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.BiasVariable.html
+[BiasVariable]:       http://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.BiasVariable.html
 [CMS Cookiecutter]:   https://github.com/molssi/cookiecutter-cms
-[CustomCVForce]:      https://docs.openmm.org/latest/api-python/generated/openmm.openmm.CustomCVForce.html
-[Force]:              https://docs.openmm.org/latest/api-python/generated/openmm.openmm.Force.html
-[Metadynamics]:       https://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.Metadynamics.html
-[OpenMM]:             https://openmm.org
+[CustomCVForce]:      http://docs.openmm.org/latest/api-python/generated/openmm.openmm.CustomCVForce.html
+[Force]:              http://docs.openmm.org/latest/api-python/generated/openmm.openmm.Force.html
+[Metadynamics]:       http://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.Metadynamics.html
+[OpenMM]:             http://openmm.org
 
 [Angle]:                  https://redesignscience.github.io/cvpack/latest/api/Angle.html
 [Atomic Function]:        https://redesignscience.github.io/cvpack/latest/api/AtomicFunction.html

cvpack/utils.py

@@ -179,7 +179,7 @@ def compute_effective_mass(
     squared_forces = np.sum(np.square(force_vectors), axis=1)
     nonzeros = np.nonzero(squared_forces)[0]
     if nonzeros.size == 0:
-        return mmunit.Quantity(np.inf, force._mass_unit)
+        return np.inf
     mass_values = np.fromiter(map(get_mass, nonzeros), dtype=np.float64)
     return 1.0 / np.sum(squared_forces[nonzeros] / mass_values)
 

devtools/conda-recipes/anaconda/meta.yaml

@@ -31,12 +31,12 @@ test:
 about:
   home: https://github.com/RedesignScience/cvpack
   summary: Useful Collective Variables for OpenMM
+  description: Useful Collective Variables for OpenMM
   license: MIT
   license_family: MIT
   license_file: LICENSE
   doc_url: https://redesignscience.github.io/cvpack/latest
   dev_url: https://github.com/RedesignScience/cvpack
-
 extra:
   recipe-maintainers:
     - craabreu

docs/getting_started.rst

@@ -73,12 +73,12 @@ The output should be::
 The output shows that the normalized helix content of residues LYS60-ARG80 of the T4 lysozyme L99A
 molecule is close to one, as expected, no matter which measure is used.
 
-.. _BiasVariable:       https://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.BiasVariable.html
-.. _CollectiveVariable: https://ufedmm.readthedocs.io/en/latest/pythonapi/ufedmm.html#ufedmm.ufedmm.CollectiveVariable
-.. _Context:            https://docs.openmm.org/latest/api-python/generated/openmm.openmm.Context.html
-.. _CustomCVForce:      https://docs.openmm.org/latest/api-python/generated/openmm.openmm.CustomCVForce.html
-.. _Force:              https://docs.openmm.org/latest/api-python/generated/openmm.openmm.Force.html
-.. _Metadynamics:       https://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.Metadynamics.html
-.. _OpenMM:             https://openmm.org
+.. _BiasVariable:       http://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.BiasVariable.html
+.. _CollectiveVariable: https://craabreu.github.io/ufedmm/pythonapi/ufedmm.html#ufedmm.ufedmm.CollectiveVariable
+.. _Context:            http://docs.openmm.org/latest/api-python/generated/openmm.openmm.Context.html
+.. _CustomCVForce:      http://docs.openmm.org/latest/api-python/generated/openmm.openmm.CustomCVForce.html
+.. _Force:              http://docs.openmm.org/latest/api-python/generated/openmm.openmm.Force.html
+.. _Metadynamics:       http://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.Metadynamics.html
+.. _OpenMM:             http://openmm.org
 .. _OpenMMTools:        https://openmmtools.readthedocs.io/en/stable
-.. _UFED:               https://ufedmm.readthedocs.io/en/latest/index.html
+.. _UFED:               https://craabreu.github.io/ufedmm/