Switch to L-BFGS and fixup GFN-FF parsing

Signed-off-by: Geoff Hutchison <[email protected]>
OpenChemistry · Oct 24, 2023 · 857c54e · 857c54e
1 parent 3c58251
commit 857c54e
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Showing 5 changed files with 11 additions and 8 deletions.
diff --git a/avogadro/qtplugins/forcefield/forcefield.cpp b/avogadro/qtplugins/forcefield/forcefield.cpp
@@ -205,7 +205,8 @@ void Forcefield::optimize()
   bool isInteractive = m_molecule->undoMolecule()->isInteractive();
   m_molecule->undoMolecule()->setInteractive(true);
 
-  cppoptlib::ConjugatedGradientDescentSolver<EnergyCalculator> solver;
+  cppoptlib::LbfgsSolver<EnergyCalculator> solver;
+  // cppoptlib::ConjugatedGradientDescentSolver<EnergyCalculator> solver;
 
   int n = m_molecule->atomCount();
 

diff --git a/avogadro/qtplugins/forcefield/scriptenergy.cpp b/avogadro/qtplugins/forcefield/scriptenergy.cpp
@@ -125,9 +125,11 @@ Real ScriptEnergy::value(const Eigen::VectorXd& x)
   double energy = 0.0;
   for (auto line : lines) {
     if (line.startsWith("AvogadroEnergy:")) {
-      QStringList items = line.split(" ");
-      if (items.size() > 1)
+      QStringList items = line.split(" ", QString::SkipEmptyParts);
+      if (items.size() > 1) {
         energy = items[1].toDouble();
+        break;
+      }
     }
   }
 
@@ -163,7 +165,7 @@ void ScriptEnergy::gradient(const Eigen::VectorXd& x, Eigen::VectorXd& grad)
     }
 
     if (readingGrad) {
-      QStringList items = line.split(" ");
+      QStringList items = line.split(" ", QString::SkipEmptyParts);
       if (items.size() == 3) {
         grad[i] = items[0].toDouble();
         grad[i + 1] = items[1].toDouble();

diff --git a/avogadro/qtplugins/forcefield/scripts/gfn1.py b/avogadro/qtplugins/forcefield/scripts/gfn1.py
@@ -64,7 +64,7 @@ def run(filename):
     while(True):
         # read new coordinates from stdin
         for i in range(len(atoms)):
-            coordinates[i] = np.fromstring(input(), sep=" ")
+            coordinates[i] = np.fromstring(input())
         # .. convert from Angstrom to Bohr
         coordinates /= 0.52917721067
 

diff --git a/avogadro/qtplugins/forcefield/scripts/gfn2.py b/avogadro/qtplugins/forcefield/scripts/gfn2.py
@@ -64,7 +64,7 @@ def run(filename):
     while(True):
         # read new coordinates from stdin
         for i in range(len(atoms)):
-            coordinates[i] = np.fromstring(input(), sep=" ")
+            coordinates[i] = np.fromstring(input())
         # .. convert from Angstrom to Bohr
         coordinates /= 0.52917721067
 

diff --git a/avogadro/qtplugins/forcefield/scripts/gfnff.py b/avogadro/qtplugins/forcefield/scripts/gfnff.py
@@ -66,7 +66,7 @@ def run(filename):
     while True:
         # read new coordinates from stdin
         for i in range(len(atoms)):
-            coordinates[i] = np.fromstring(input(), sep=" ")
+            coordinates[i] = np.fromstring(input())
         # .. convert from Angstrom to Bohr
         coordinates /= 0.52917721067
 
@@ -80,7 +80,7 @@ def run(filename):
         # now print the gradient
         # .. we don't want the "[]" in the output
         print("AvogadroGradient:")
-        grad = res.get_gradient() * 496100.475  # convert units
+        grad = res.get_gradient() * 4961.475  # convert units
         output = np.array2string(grad)
         output = output.replace("[", "").replace("]", "")
         print(output)