Merge pull request #386 from OpenBioSim/backport_384

Backport fixes from PR #384

Author: lohedges

doc/source/changelog.rst

@@ -12,6 +12,15 @@ Development was migrated into the
 `OpenBioSim <https://github.com/openbiosim>`__
 organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 
+`2025.4.0 <https://github.com/openbiosim/sire/compare/2025.3.0...2025.4.0>`__ - December 2025
+---------------------------------------------------------------------------------------------
+
+* Please add an item to this CHANGELOG for any new features or bug fixes when creating a PR.
+
+* Use ``"0"`` for null EMLE interpolation force since ``""`` causes issues on some platforms.
+
+* Fix ``delta`` parameter in soft-core Coulomb potential.
+
 `2025.3.0 <https://github.com/openbiosim/sire/compare/2025.2.0...2025.3.0>`__ - November 2025
 ---------------------------------------------------------------------------------------------
 

doc/source/tutorial/part07/03_ghosts.rst

@@ -68,15 +68,15 @@ It is based on the following electrostatic and Lennard-Jones potentials:
 
 .. math::
 
-   V_{\text{elec}}(r) = q_i q_j \left[ \frac{(1 - \alpha)^n}{\sqrt{r^2 + \delta_\text{coulomb}^2}} - \frac{\kappa}{r} \right]
+   V_{\text{elec}}(r) = q_i q_j \left[ \frac{(1 - \alpha)^n}{\sqrt{r^2 + \delta_\text{coulomb}}} - \frac{\kappa}{r} \right]
 
    V_{\text{LJ}}(r) = 4\epsilon \left[ \frac{\sigma^{12}}{(\delta_\text{LJ} \sigma + r^2)^6} - \frac{\sigma^6}{(\delta_\text{LJ} \sigma + r^2)^3} \right]
 
 where
 
 .. math::
 
-    \delta_\text{coulomb} = \alpha \times \text{shift_coulomb}
+    \delta_\text{coulomb} = \alpha \times \text{shift_coulomb}^2
 
     \delta_\text{LJ} = \alpha \times \text{shift_LJ}
 

src/sire/qm/_emle.py

@@ -45,7 +45,7 @@ def get_forces(self):
 
         # Create a null CustomBondForce to add the EMLE interpolation
         # parameter.
-        interpolation_force = _CustomBondForce("")
+        interpolation_force = _CustomBondForce("0")
         interpolation_force.addGlobalParameter("lambda_emle", 1.0)
 
         # Return the forces.
@@ -94,7 +94,7 @@ def get_forces(self):
 
         # Create a null CustomBondForce to add the EMLE interpolation
         # parameter.
-        interpolation_force = _CustomBondForce("")
+        interpolation_force = _CustomBondForce("0")
         interpolation_force.addGlobalParameter("lambda_emle", 1.0)
 
         # Return the forces.

wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp

@@ -1359,7 +1359,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system,
         {
             nb14_expression = QString(
                                   "coul_nrg+lj_nrg;"
-                                  "coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha*alpha)+r_safe^2))-(kappa/r_safe));"
+                                  "coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha)+r_safe^2))-(kappa/r_safe));"
                                   "lj_nrg=four_epsilon*sig6*(sig6-1);"
                                   "sig6=(sigma^6)/(%3*sigma^6 + r_safe^6);"
                                   "r_safe=max(r, 0.001);")
@@ -1372,7 +1372,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system,
         {
             nb14_expression = QString(
                                   "coul_nrg+lj_nrg;"
-                                  "coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha*alpha)+r_safe^2))-(kappa/r_safe));"
+                                  "coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha)+r_safe^2))-(kappa/r_safe));"
                                   "lj_nrg=four_epsilon*sig6*(sig6-1);"
                                   "sig6=(sigma^6)/(((sigma*delta) + r_safe^2)^3);"
                                   "r_safe=max(r, 0.001);"
@@ -1420,7 +1420,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system,
             // kJ mol-1 given the units of charge (|e|) and distance (nm)
             //
             clj_expression = QString("coul_nrg+lj_nrg;"
-                                     "coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha*max_alpha)+r_safe^2))-(max_kappa/r_safe));"
+                                     "coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha)+r_safe^2))-(max_kappa/r_safe));"
                                      "lj_nrg=two_sqrt_epsilon1*two_sqrt_epsilon2*sig6*(sig6-1);"
                                      "sig6=(sigma^6)/(%3*sigma^6 + r_safe^6);"
                                      "r_safe=max(r, 0.001);"
@@ -1458,7 +1458,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system,
             // kJ mol-1 given the units of charge (|e|) and distance (nm)
             //
             clj_expression = QString("coul_nrg+lj_nrg;"
-                                     "coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha*max_alpha)+r_safe^2))-(max_kappa/r_safe));"
+                                     "coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha)+r_safe^2))-(max_kappa/r_safe));"
                                      "lj_nrg=two_sqrt_epsilon1*two_sqrt_epsilon2*sig6*(sig6-1);"
                                      "sig6=(sigma^6)/(((sigma*delta) + r_safe^2)^3);"
                                      "delta=%3*max_alpha;"