Fixed problem - gradients went the wrong way

Signed-off-by: Geoff Hutchison <[email protected]>
OpenChemistry · Oct 23, 2023 · f2e416f · f2e416f
1 parent 10d7d40
commit f2e416f
Show file tree

Hide file tree

Showing 5 changed files with 17 additions and 17 deletions.
diff --git a/avogadro/calc/energycalculator.cpp b/avogadro/calc/energycalculator.cpp
@@ -26,12 +26,10 @@ void EnergyCalculator::cleanGradients(TVector& grad)
   }
 
   // freeze any masked atoms or coordinates
-  /*
   if (m_mask.rows() == size)
     grad = grad.cwiseProduct(m_mask);
   else
     std::cerr << "Error: mask size " << m_mask.rows() << " " << grad.rows() << std::endl;
-  */
 }
 
 } // namespace Avogadro
diff --git a/avogadro/qtgui/pythonscript.cpp b/avogadro/qtgui/pythonscript.cpp
@@ -224,8 +224,8 @@ void PythonScript::processFinished(int, QProcess::ExitStatus)
 void PythonScript::asyncTerminate()
 {
   if (m_process != nullptr) {
-    m_process->terminate();
     disconnect(m_process, SIGNAL(finished()), this, SLOT(processFinished()));
+    m_process->kill();
     m_process->deleteLater();
     m_process = nullptr;
   }

diff --git a/avogadro/qtplugins/forcefield/CMakeLists.txt b/avogadro/qtplugins/forcefield/CMakeLists.txt
@@ -16,9 +16,12 @@ target_link_libraries(Forcefield PRIVATE Avogadro::Calc)
 
 # Bundled forcefield scripts
 set(forcefields
+  scripts/gaff.py
   scripts/gfn1.py
   scripts/gfn2.py
   scripts/gfnff.py
+  scripts/mmff94.py
+  scripts/uff.py
 )
 
 install(PROGRAMS ${forcefields}

diff --git a/avogadro/qtplugins/forcefield/forcefield.cpp b/avogadro/qtplugins/forcefield/forcefield.cpp
@@ -29,9 +29,8 @@
 
 #include <cppoptlib/meta.h>
 #include <cppoptlib/problem.h>
-
+#include <cppoptlib/solver/bfgssolver.h>
 #include <cppoptlib/solver/lbfgssolver.h>
-// not currently used
 #include <cppoptlib/solver/conjugatedgradientdescentsolver.h>
 #include <cppoptlib/solver/gradientdescentsolver.h>
 
@@ -125,9 +124,8 @@ void Forcefield::optimize()
   bool isInteractive = m_molecule->undoMolecule()->isInteractive();
   m_molecule->undoMolecule()->setInteractive(true);
 
-  //cppoptlib::LbfgsSolver<EnergyCalculator> solver;
-  //cppoptlib::ConjugatedGradientDescentSolver<EnergyCalculator> solver;
-  cppoptlib::GradientDescentSolver<EnergyCalculator> solver;
+  cppoptlib::ConjugatedGradientDescentSolver<EnergyCalculator> solver;
+  //cppoptlib::GradientDescentSolver<EnergyCalculator> solver;
 
   int n = m_molecule->atomCount();
   // we have to cast the current 3d positions into a VectorXd
@@ -146,17 +144,17 @@ void Forcefield::optimize()
   cppoptlib::Criteria<Real> crit = cppoptlib::Criteria<Real>::defaults();
 
   // e.g., every N steps, update coordinates
-  crit.iterations = 10;
+  crit.iterations = m_nSteps;
   // we don't set function or gradient criteria
   // .. these seem to be broken in the solver code
   // .. so we handle ourselves
   solver.setStopCriteria(crit);
 
   // set the method
-  std::string recommended = "MMFF94";
+  std::string recommended = recommendedForceField();
   qDebug() << "Energy method: " << recommended.c_str();
 
-  if (m_method == nullptr) {
+  if (m_method == nullptr || m_method->identifier() != recommended) {
     // we have to create the calculator
     m_method = Calc::EnergyManager::instance().model(recommended);
   }
@@ -181,6 +179,8 @@ void Forcefield::optimize()
   for (unsigned int i = 0; i < m_maxSteps / crit.iterations; ++i) {
     solver.minimize(*m_method, positions);
 
+    qApp->processEvents(QEventLoop::AllEvents, 500);
+
     currentEnergy = m_method->value(positions);
     // get the current gradient for force visualization
     m_method->gradient(positions, gradient);
@@ -204,7 +204,7 @@ void Forcefield::optimize()
         pos[i] = Vector3(*(d), *(d + 1), *(d + 2));
         d += 3;
 
-        forces[i] = -1.0 * Vector3(gradient[3 * i], gradient[3 * i + 1],
+        forces[i] = -0.1 * Vector3(gradient[3 * i], gradient[3 * i + 1],
                                    gradient[3 * i + 2]);
       }
     }
@@ -246,7 +246,7 @@ void Forcefield::energy()
   std::string recommended = recommendedForceField();
   qDebug() << "Energy method: " << recommended.c_str();
 
-  if (m_method == nullptr) {
+  if (m_method == nullptr || m_method->identifier() != recommended) {
     // we have to create the calculator
     m_method = Calc::EnergyManager::instance().model(recommended);
   }

diff --git a/avogadro/qtplugins/forcefield/scriptenergy.cpp b/avogadro/qtplugins/forcefield/scriptenergy.cpp
@@ -154,7 +154,6 @@ void ScriptEnergy::gradient(const Eigen::VectorXd& x, Eigen::VectorXd& grad)
   // parse the result
   // first split on newlines
   QStringList lines = QString(result).remove('\r').split('\n');
-  double energy = 0.0;
   unsigned int i = 0;
   bool readingGrad = false;
   for (auto line : lines) {
@@ -166,9 +165,9 @@ void ScriptEnergy::gradient(const Eigen::VectorXd& x, Eigen::VectorXd& grad)
     if (readingGrad) {
       QStringList items = line.split(" ");
       if (items.size() == 3) {
-        grad[i] = items[0].toDouble();
-        grad[i + 1] = items[1].toDouble();
-        grad[i + 2] = items[2].toDouble();
+        grad[i] = -1.0*items[0].toDouble();
+        grad[i + 1] = -1.0*items[1].toDouble();
+        grad[i + 2] = -1.0*items[2].toDouble();
         i += 3;
       }