Changeset 79cd79 for molecuilder/src/molecules.cpp

Timestamp:

Sep 9, 2008, 8:37:07 AM (17 years ago)

Author:

Frederik Heber <heber@…>

Children:

8e52aa

Parents:

ec4e84

Message:

new function: molecule::OutputTemperatureFromTrajectories() stores velocities as temperature

In order to use VibrAlyzer we need a temperature file, which we don't have anymore as we do the M
D in molecuilder now. Hence, there is a new command line switch (-L) and a menu item in MeasureAt
oms() in order to print temperature or to store it to a given file.

File:

• molecuilder/src/molecules.cpp (modified) (1 diff)

molecuilder/src/molecules.cpp

@@ -4664 +4664 @@
 };
 
+/** Stores the temperature evaluated from velocities in molecule::Trajectories.
+ * We simply use the formula equivaleting temperature and kinetic energy:
+ * \f$k_B T = \sum_i m_i v_i^2\f$
+ * \param *out output stream for debugging
+ * \param startstep first MD step in molecule::Trajectories
+ * \param endstep last plus one MD step in molecule::Trajectories
+ * \param *output output stream of temperature file
+ * \return file written (true), failure on writing file (false)
+ */ 
+bool molecule::OutputTemperatureFromTrajectories(ofstream *out, int startstep, int endstep, ofstream *output)
+{
+  double temperature;
+  atom *Walker = NULL;
+  // test stream
+  if (output == NULL)
+    return false;
+  else 
+    *output << "# Step Temperature [K] Temperature [a.u.]" << endl;
+  for (int step=startstep;step < endstep; step++) { // loop over all time steps
+    temperature = 0.;
+    Walker = start;
+    while (Walker->next != end) {
+      Walker = Walker->next;
+      for (int i=NDIM;i--;)
+        temperature += Walker->type->mass * Trajectories[Walker].U.at(step).x[i]* Trajectories[Walker].U.at(step).x[i];
+    }
+    *output << step << "\t" << temperature*AtomicEnergyToKelvin << "\t" << temperature << endl;
+  }
+  return true;
+};