git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11447 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/colvars/abf_data.h

@@ -0,0 +1,94 @@
+/// \file integrate.h General headers for ABF_integrate
+
+#include <iostream>
+#include <vector>
+
+#define MIN_SAMPLES 1
+
+/// Free energy gradients class
+class ABFdata {
+
+  protected:
+    /// Sizes of (i-1) dimension blocks
+    /// computed as Prod_(j<i) sizes[j]
+    int *blocksizes;
+    /// Minimum values of each variable
+    double *mins;
+
+  public:
+    int Nvars;
+    /// Free energy gradients (vector field)
+    double *gradients;
+    /// Sampling from the ABF calculation
+    unsigned int *count;
+    /// Bin widths
+    double *widths;
+
+    unsigned int scalar_dim;
+    unsigned int vec_dim;
+    unsigned int *histogram;
+
+    /// History-dependent bias
+    double *bias;
+
+    /// Estimate of the FE gradient computed
+    /// from MtD bias or histogram in standard MC
+    double *estimate;
+
+    /// Deviation between starting free energy gradient and 
+    /// estimated one
+    double *deviation;
+
+    void write_histogram(const char *fileName);
+    void write_bias(const char *fileName);
+    void write_field(double *field, const char *fileName);
+
+    /// Grid sizes
+    int *sizes;
+
+    /// Flag stating if each variable is periodic
+    int *PBC;
+
+    /// Constructor: reads from a file
+     ABFdata(const char *gradFileName);
+    ~ABFdata();
+
+    /// \brief Returns an offset for scalar fields based on a n-index.
+    /// multiply by Nvars to get an offset in a Nvars-vector field
+    unsigned int offset(const int *);
+
+    inline bool wrap(int &pos, int i);
+
+    /// Decides if an offset is outside the allowed region based on the ABF sampling
+    inline bool allowed(unsigned int offset);
+};
+
+
+inline bool ABFdata::wrap(int &pos, int i)
+{
+    if (PBC[i]) {
+        if (pos == -1) {
+            pos = sizes[i] - 1;
+            return true;
+        }
+        if (pos == sizes[i]) {
+            pos = 0;
+            return true;
+        }
+    } else {
+        // No PBC
+        if (pos == -1) {
+            pos = 0;
+            return false;
+        }
+        if (pos == sizes[i]) {
+            pos = sizes[i] - 1;
+            return false;
+        }
+    }
+    return true;
+}
+
+inline bool ABFdata::allowed(unsigned int offset) {
+    return count[offset] > MIN_SAMPLES;
+}