Merge pull request #9 from gg27fyla/master

some changes

Author: conradhuebler

Diff for: src/capabilities/simplemd.cpp

@@ -168,6 +168,7 @@ void SimpleMD::LoadControlJson()
     m_T0 = Json2KeyWord<double>(m_defaults, "T");
     m_rmrottrans = Json2KeyWord<int>(m_defaults, "rmrottrans");
     m_nocenter = Json2KeyWord<bool>(m_defaults, "nocenter");
+    m_COM = Json2KeyWord<bool>(m_defaults, "COM");
     m_dump = Json2KeyWord<int>(m_defaults, "dump");
     m_print = Json2KeyWord<int>(m_defaults, "print");
     m_max_top_diff = Json2KeyWord<int>(m_defaults, "MaxTopoDiff");
@@ -339,7 +340,7 @@ bool SimpleMD::Initialise()
     m_molecule.setCharge(0);
     if (!m_nocenter) {
         std::cout << "Move stucture to the origin ... " << std::endl;
-        m_molecule.setGeometry(GeometryTools::TranslateGeometry(m_molecule.getGeometry(), GeometryTools::Centroid(m_molecule.getGeometry()), Position{ 0, 0, 0 }));
+        m_molecule.Center(m_COM);
     } else
         std::cout << "Move stucture NOT to the origin ... " << std::endl;
 
@@ -714,6 +715,7 @@ nlohmann::json SimpleMD::WriteRestartInformation()
     restart["gradient"] = Tools::DoubleVector2String(m_gradient);
     restart["rmrottrans"] = m_rmrottrans;
     restart["nocenter"] = m_nocenter;
+    restart["COM"] = m_COM;
     restart["average_T"] = m_aver_Temp;
     restart["average_Epot"] = m_aver_Epot;
     restart["average_Ekin"] = m_aver_Ekin;
@@ -819,6 +821,10 @@ bool SimpleMD::LoadRestartInformation(const json& state)
         m_nocenter = state["nocenter"];
     } catch (json::type_error& e) {
     }
+    try {
+        m_COM = state["COM"];
+    } catch (json::type_error& e) {
+    }
     try {
         m_T0 = state["T"];
     } catch (json::type_error& e) {
@@ -1109,6 +1115,12 @@ void SimpleMD::start()
             }
         }
 
+/////////// Dipole calc
+
+
+
+
+/////////// Dipole calc
         if (m_step % m_dump == 0) {
             bool write = WriteGeometry();
             if (write) {

Diff for: src/capabilities/simplemd.h

@@ -130,6 +130,7 @@ static json CurcumaMDJson{
     { "Spin", 0 },
     { "rmrottrans", 0 },
     { "nocenter", false },
+    { "COM", false },
     { "dump", 50 },
     { "print", 1000 },
     { "unique", false },
@@ -307,6 +308,7 @@ class SimpleMD : public CurcumaMethod {
     bool m_initialised = false, m_restart = false, m_writeUnique = true, m_opt = false, m_rescue = false, m_writeXYZ = true, m_writeinit = false, m_norestart = false;
     int m_rmrottrans = 0, m_rattle_maxiter = 100;
     bool m_nocenter = false;
+    bool m_COM = false;
     bool m_wall_render = false;
     EnergyCalculator* m_interface;
     RMSDTraj* m_unqiue;

Diff for: src/main.cpp

@@ -953,9 +953,11 @@ int main(int argc, char **argv) {
             while (!file.AtEnd()) { // calculation and output dipole moment
                 mol = file.Next(); // load Molecule
                 mol.Center(false);
+
                 EnergyCalculator interface("gfn2", blob); // set method to gfn2-xtb and give
                 interface.setMolecule(mol); // set molecule for calc
                 interface.CalculateEnergy(false, true); // calc energy and charges and dipole moment
+
                 mol.setPartialCharges(interface.Charges()); // calc Partial Charges and give it to mol
                 auto charges = interface.Charges(); // dec and init charges
                 mol.setDipole(interface.Dipole() * au);