more documentation in header files

Author: Trombach

acceptanceTest.h

@@ -1,6 +1,10 @@
 #ifndef ACCEPTANCETEST
 #define ACCEPTANCETEST
 
+/*
+Acceptance test for basinhopping step.  
+*/
+
 class AcceptanceTest
 {
     protected:

basinhopping.h

@@ -7,6 +7,44 @@
 #include "acceptanceTest.h"
 #include "storage.h"
 
+/*
+This class implements monte-carlo basin hopping and stores unique local minima.
+
+Implementations can be found in "basinhopping.cc".
+
+Parameters
+----------
+
+const structure _initialCoordinates :
+    saves coordinates of initial structure
+structure _currentStep :
+    saves coordinates of current step
+structure _previousStep :
+    saves coordinates of previous step
+const int _size :
+    equal to the number of atoms in the initialising structure
+const int _nsteps :
+    maximum number of basinhopping steps
+std::shared_ptr<AcceptanceTest> _accept :
+    acceptance test. See "acceptanceTest.h".
+T _uniqueStructures :
+    storage for unique structures. See "storage.h".
+bool _accepted :
+    true if Monte-Carlo step was accepted, false if otherwise.
+unsigned int _iteration :
+    current number of iterations.
+unsigned int _naccept :
+    number of accepted configurations (structures).
+unsigned int _nattempts :
+    number of times the stepsize was attempted to be updated.
+unsigned int _nsame :
+    number of times the same structure has been found.
+int _interval :
+    number of steps that defines how often temperature and stepsize should be adjusted.
+double _stepScale :
+    scaling parameter for the stepsize. dynamically adjusted.
+*/
+
 template <typename T>
 class BasinHopping
 {

iop.h

@@ -7,6 +7,11 @@
 #include "structure.h"
 #include "parameter.h"
 
+/*
+Functions concerning input and output.
+
+Implementations can be found in "iop.cc".
+*/
 
 void xyzout (structure &outputStructure, const std::string &name = "structure.xyz");
 void xyzoutall (std::vector<structure> &outputStructures, const std::string &name = "all.xyz");

lina.h

@@ -4,6 +4,12 @@
 #include <vector>
 #include "geometry.h"
 
+/*
+Functions for diagonalisations.
+
+Implementations can be found in "dlib-lina.cc".
+*/
+
 std::vector<double> diag (std::vector< std::vector<double> > &matrix);
 std::vector<std::pair<double, std::vector<double> > > diagv (std::vector< std::vector<double> > &matrix);
 matrix3d m3d_diagv (matrix3d &matrix);

parameter.h

@@ -4,6 +4,10 @@
 #include <string>
 #include <map>
 
+/*
+Simple class to store parameters.
+*/
+
 template <typename T> class parameter
 {
 

stop_strategy.h

@@ -7,7 +7,7 @@
 #include <dlib/algs.h>
 
 /*
-    This class implements a slightly modified stop strategy for the dlib mnimiser.
+This class implements a slightly modified stop strategy for the dlib mnimiser.
 */
 
 namespace dlib {

timer.h

@@ -3,6 +3,19 @@
 
 #include <ctime>
 
+/*
+Simple class to calculate program timings.
+
+Usage
+-----
+
+* call the constructor at the start of the function you want to time
+
+* to get the current runtime between timing()-calls call timing()
+
+* The total runtime can be accessed by calling total_timing()
+
+*/
 
 //creates object that can keep track of time in program
 class timer 

transversePotential.h

@@ -3,6 +3,23 @@
 #include "structure.h"
 #include "globals.h"
 
+/*
+This class wraps a potential and removes the gradient in one direction.
+
+Implementations can be found in "transversePotential.cc".
+
+Parameters
+----------
+
+pairPotential* _potential :
+    potential object. "See potential.h". Should be passed as a shared_ptr.
+column_vector _vector :
+    direction to be removed from the gradient
+double _eval :
+    if _vector corresponds to an eigenvector of the hessian matrix, this can be
+    used to track store the eigenvalue.
+*/
+
 class TransversePotential
 {
     private: