replace some vector/array matrices with eigen matrices

Signed-off-by: Conrad Hübler <[email protected]>
conradhuebler · Mar 5, 2024 · a32acc5 · a32acc5
1 parent a1d8d55
commit a32acc5
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Showing 9 changed files with 154 additions and 110 deletions.
diff --git a/src/capabilities/curcumaopt.cpp b/src/capabilities/curcumaopt.cpp
@@ -134,7 +134,7 @@ void CurcumaOpt::ProcessMoleculesSerial(const std::vector<Molecule>& molecules)
 #endif
 
         if (m_hessian) {
-            Hessian hess(m_method, m_defaults, m_threads);
+            Hessian hess(m_method, m_defaults, false);
             hess.setMolecule(*iter);
             hess.CalculateHessian(m_hessian);
         }
@@ -191,7 +191,7 @@ void CurcumaOpt::ProcessMolecules(const std::vector<Molecule>& molecules)
 
         Molecule* mol2 = new Molecule(thread->getMolecule());
         if (m_hessian) {
-            Hessian hess(m_method, m_defaults, m_threads);
+            Hessian hess(m_method, m_defaults, false);
             hess.setMolecule(mol2);
             hess.CalculateHessian(m_hessian);
         }

diff --git a/src/capabilities/hessian.cpp b/src/capabilities/hessian.cpp
@@ -68,17 +68,17 @@ void HessianThread::Numerical()
     m_geom_ip_jm = m_molecule.Coords();
     m_geom_im_jm = m_molecule.Coords();
 
-    m_geom_ip_jp[m_i][m_xi] += m_d;
-    m_geom_ip_jp[m_j][m_xj] += m_d;
+    m_geom_ip_jp(m_i, m_xi) += m_d;
+    m_geom_ip_jp(m_j, m_xj) += m_d;
 
-    m_geom_im_jp[m_i][m_xi] -= m_d;
-    m_geom_im_jp[m_j][m_xj] += m_d;
+    m_geom_im_jp(m_i, m_xi) -= m_d;
+    m_geom_im_jp(m_j, m_xj) += m_d;
 
-    m_geom_ip_jm[m_i][m_xi] += m_d;
-    m_geom_ip_jm[m_j][m_xj] -= m_d;
+    m_geom_ip_jm(m_i, m_xi) += m_d;
+    m_geom_ip_jm(m_j, m_xj) -= m_d;
 
-    m_geom_im_jm[m_i][m_xi] -= m_d;
-    m_geom_im_jm[m_j][m_xj] -= m_d;
+    m_geom_im_jm(m_i, m_xi) -= m_d;
+    m_geom_im_jm(m_j, m_xj) -= m_d;
 
     EnergyCalculator energy(m_method, m_controller);
     energy.setMolecule(m_molecule);
@@ -104,7 +104,7 @@ void HessianThread::Seminumerical()
     m_geom_ip_jp = m_molecule.Coords();
     m_geom_im_jp = m_molecule.Coords();
 
-    m_geom_ip_jp[m_i][m_xi] += m_d;
+    m_geom_ip_jp(m_i, m_xi) += m_d;
     // std::cout << m_controller << std::endl;
 
     EnergyCalculator energy(m_method, m_controller);
@@ -115,7 +115,7 @@ void HessianThread::Seminumerical()
     energy.CalculateEnergy(true, false);
     Matrix gradientp = energy.Gradient();
 
-    m_geom_im_jp[m_i][m_xi] -= m_d;
+    m_geom_im_jp(m_i, m_xi) -= m_d;
 
     energy.updateGeometry(m_geom_im_jp);
     energy.CalculateEnergy(true, false);
@@ -130,7 +130,7 @@ Hessian::Hessian(const std::string& method, const json& controller, bool silent)
 
 {
     UpdateController(controller);
-    m_threads = m_controller["threads"];
+    m_threads = m_defaults["threads"];
     /* Yeah, thats not really correct, but it works a bit */
     if (m_method.compare("gfnff") == 0) {
         m_scale_functions = [](double val) -> double {

diff --git a/src/capabilities/hessian.h b/src/capabilities/hessian.h
@@ -71,7 +71,7 @@ class HessianThread : public CxxThread {
     json m_controller, m_parameter;
     Molecule m_molecule;
     Matrix m_gradient;
-    std::vector<std::array<double, 3>> m_geom_ip_jp, m_geom_im_jp, m_geom_ip_jm, m_geom_im_jm;
+    Geometry m_geom_ip_jp, m_geom_im_jp, m_geom_ip_jm, m_geom_im_jm;
     int m_i, m_j, m_xi, m_xj;
     bool m_fullnumerical = true;
     double m_dd = 0;

diff --git a/src/core/energycalculator.cpp b/src/core/energycalculator.cpp
@@ -285,6 +285,18 @@ void EnergyCalculator::updateGeometry(const std::vector<double>& geometry)
     }
     // m_containsNaN = std::isnan(m_geometry[m_atoms - 1][0]);
 }
+
+void EnergyCalculator::updateGeometry(const Matrix& geometry)
+{
+    m_geometry = geometry;
+    for (int i = 0; i < m_atoms; ++i) {
+        m_coord[3 * i + 0] = geometry(i, 0) / au;
+        m_coord[3 * i + 1] = geometry(i, 1) / au;
+        m_coord[3 * i + 2] = geometry(i, 2) / au;
+    }
+}
+
+/*
 void EnergyCalculator::updateGeometry(const std::vector<std::array<double, 3>>& geometry)
 {
     for (int i = 0; i < m_atoms; ++i) {
@@ -297,7 +309,7 @@ void EnergyCalculator::updateGeometry(const std::vector<std::array<double, 3>>&
         m_geometry(i, 2) = geometry[i][2];
     }
 }
-
+*/
 double EnergyCalculator::CalculateEnergy(bool gradient, bool verbose)
 {
     m_ecengine(gradient, verbose);

diff --git a/src/core/energycalculator.h b/src/core/energycalculator.h
@@ -56,8 +56,8 @@ class EnergyCalculator {
     void updateGeometry(const double* coord);
     void updateGeometry(const std::vector<double>& geometry);
 
-    void updateGeometry(const std::vector<std::array<double, 3>>& geometry);
-
+    // void updateGeometry(const std::vector<std::array<double, 3>>& geometry);
+    void updateGeometry(const Matrix& geometry);
     void updateGeometry(const Eigen::VectorXd& geometry);
 
     void getGradient(double* coord);

diff --git a/src/core/forcefield.cpp b/src/core/forcefield.cpp
@@ -30,7 +30,7 @@ ForceField::ForceField(const json& controller)
 {
     m_threadpool = new CxxThreadPool();
     m_threadpool->setProgressBar(CxxThreadPool::ProgressBarType::None);
-    m_threads = 16;
+    m_threads = 1;
 }
 
 void ForceField::UpdateGeometry(const Matrix& geometry)