Merge pull request #1674 from ghutchis/add-cjson-atom-forces

Add support for reading and writing atom force vectors

avogadro/io/cjsonformat.cpp

@@ -159,7 +159,16 @@ bool CjsonFormat::deserialize(std::istream& file, Molecule& molecule,
     }
   }
 
-  // todo? 2d position
+  // Array of vector3 for forces if available
+  json forces = atoms["forces"];
+  if (isNumericArray(forces) && forces.size() == 3 * atomCount) {
+    for (Index i = 0; i < atomCount; ++i) {
+      auto a = molecule.atom(i);
+      a.setForceVector(
+        Vector3(forces[3 * i], forces[3 * i + 1], forces[3 * i + 2]));
+    }
+  }
+
   // labels
   json labels = atoms["labels"];
   if (labels.is_array() && labels.size() == atomCount) {
@@ -1058,6 +1067,18 @@ bool CjsonFormat::serialize(std::ostream& file, const Molecule& molecule,
       }
       root["atoms"]["coords"]["2d"] = coords2d;
     }
+
+    // forces if present
+    const auto forceVectors = molecule.forceVectors();
+    if (forceVectors.size() == molecule.atomCount()) {
+      json forces;
+      for (const auto& force : forceVectors) {
+        forces.push_back(force.x());
+        forces.push_back(force.y());
+        forces.push_back(force.z());
+      }
+      root["atoms"]["forces"] = forces;
+    }
   }
 
   // check for atom labels