From 25c4256d0f18d8eab837eb627d82e053169ae2b0 Mon Sep 17 00:00:00 2001
From: Gerd Gehrisch <gg27fyla@student.tu-freiberg.de>
Date: Thu, 5 Sep 2024 15:22:24 +0200
Subject: [PATCH] some changes

---
 src/capabilities/simplemd.cpp | 12 +++++++++++-
 src/capabilities/simplemd.h   |  2 ++
 src/main.cpp                  |  2 +-
 3 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/capabilities/simplemd.cpp b/src/capabilities/simplemd.cpp
index ce7f178..45c3c1c 100644
--- a/src/capabilities/simplemd.cpp
+++ b/src/capabilities/simplemd.cpp
@@ -73,6 +73,7 @@ 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");
@@ -219,7 +220,7 @@ 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;
 
@@ -427,6 +428,7 @@ 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;
@@ -500,6 +502,10 @@ 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) {
@@ -719,7 +725,11 @@ void SimpleMD::start()
             }
         }
 #endif
+/////////// Dipole calc
+
+
 
+/////////// Dipole calc
         if (m_step % m_dump == 0) {
             bool write = WriteGeometry();
             if (write) {
diff --git a/src/capabilities/simplemd.h b/src/capabilities/simplemd.h
index a01efc5..80214c7 100644
--- a/src/capabilities/simplemd.h
+++ b/src/capabilities/simplemd.h
@@ -45,6 +45,7 @@ static json CurcumaMDJson{
     { "Spin", 0 },
     { "rmrottrans", 0 },
     { "nocenter", false },
+    { "COM", false },
     { "dump", 50 },
     { "print", 1000 },
     { "unique", false },
@@ -193,6 +194,7 @@ 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;
     EnergyCalculator* m_interface;
     RMSDTraj* m_unqiue;
     const std::vector<double> m_used_mass;
diff --git a/src/main.cpp b/src/main.cpp
index cd15f0d..e96d416 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -945,7 +945,7 @@ 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
+                EnergyCalculator interface("gfn2", blob); // set method to gfn2-xtb
                 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