Fixed issue in nnp-checkf (non-periodic cases)

Added tests and documentation

src/application/nnp-checkf.cpp

@@ -82,7 +82,7 @@ int main(int argc, char* argv[])
                          delta);
     if (myRank == 0)
     {
-        string fileName = "forces.out";
+        string fileName = "checkf-forces.out";
         dataset.log << strpr("Individual analytic/numeric forces will be "
                              "written to \"%s\"\n", fileName.c_str());
         outFileForces.open(fileName.c_str());
@@ -113,9 +113,10 @@ int main(int argc, char* argv[])
         appendLinesToFile(outFileForces,
                           createFileHeader(title, colSize, colName, colInfo));
 
-        fileName = "summary.out";
+        fileName = "checkf-summary.out";
         dataset.log << strpr("Per-structure summary of analytic/numeric force "
-                             "comparison will be written to \"%s\"\n",
+                             "comparison will be \n"
+                             "written to \"%s\"\n",
                              fileName.c_str());
         outFileSummary.open(fileName.c_str());
         // File header.

src/doc/sphinx/source/conf.py

@@ -20,6 +20,7 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
+import sphinx_rtd_theme
 
 # -- General configuration ------------------------------------------------
 
@@ -33,7 +34,8 @@
 extensions = [
     'breathe',
 #    'exhale',
-    'sphinx.ext.mathjax'
+    'sphinx.ext.mathjax',
+    'sphinx_rtd_theme'
 ]
 
 # Setup the breathe extension

src/doc/sphinx/source/index.rst

@@ -194,6 +194,7 @@ list of keywords is provided :ref:`here <keywords>`.
 
    tools/libnnp
    tools/nnp-atomenv
+   tools/nnp-checkf
    tools/nnp-convert
    tools/nnp-norm
    tools/nnp-predict

src/doc/sphinx/source/tools/nnp-checkf.rst

@@ -0,0 +1,79 @@
+.. _nnp-checkf:
+
+nnp-checkf
+==========
+
+This tool is useful for debugging as it computes numeric forces via the
+symmetric difference quotient (central difference) and compares it to the
+analytic forces obtained directly from n2p2's prediction. Parallelization via
+MPI is supported and it can process multiple configurations in the input file.
+
+Requirements:
+-------------
+
+The HDNNP setup, symmetry function scaling data and weight parameters are
+required in the usual files. The data file ``input.data`` may contain multiple
+configurations.
+
+* ``input.data``
+* ``input.nn``
+* ``scaling.data``
+* ``weights.???.data``
+
+Usage:
+------
+
+.. code-block:: none
+
+   mpirun -np <np> nnp-checkf <<delta>>
+
+where
+
+.. code-block:: none
+
+   <np> ........ Number of MPI processes to use.
+   <<nbins>> ... (optional) Displacement for central difference (default: 1.0e-4).
+
+The ``<<delta>>`` parameter determines the position displacement of atoms used
+for the central difference approximation of the forces. If no value is provided
+the default is :math:`\delta = 10^{-4}`.
+
+Sample screen output:
+---------------------
+
+.. code-block:: none
+
+   *** ANALYTIC/NUMERIC FORCES CHECK *********************************************
+   
+   Delta for symmetric difference quotient:   1.000E-04
+   Individual analytic/numeric forces will be written to "checkf-forces.out"
+   Per-structure summary of analytic/numeric force comparison will be
+   written to "checkf-summary.out"
+   Found 3 configurations in data file: input.data.
+   Starting loop over 3 configurations...
+   
+                          numForces meanAbsError  maxAbsError  verdict
+   -------------------------------------------------------------------
+   Configuration      1:        144    7.168E-10    2.984E-09  OK.
+   Configuration      2:        144    8.215E-10    3.212E-09  OK.
+   Configuration      3:        144    7.254E-10    2.459E-09  OK.
+   *******************************************************************************
+
+File output:
+------------
+
+*  ``checkf-forces.out``: Comparison of analytic/numeric values, each force one
+   line.
+
+*  ``checkf-summary.out``: Per-structure accumulated comparison (same as screen
+   output).
+
+Examples:
+---------
+
+* Run on 4 cores and override default :math:`\delta` value:
+
+  .. code-block:: none
+
+     mpirun -np 4 nnp-checkf 1.0E-3
+

src/libnnptrain/Dataset.cpp

@@ -938,7 +938,7 @@ size_t Dataset::prepareNumericForces(Structure& original, double delta)
                 s.comment = strpr("%zu %zu %zu %d", count, iAtom, ixyz, sign);
                 // Modify atom position.
                 s.atoms.at(iAtom).r[ixyz] += sign * delta;
-                s.remap(s.atoms.at(iAtom));
+                if (s.isPeriodic) s.remap(s.atoms.at(iAtom));
             }
             count++;
         }

test/cpp/Example_nnp_checkf.h

@@ -0,0 +1,29 @@
+#ifndef EXAMPLE_NNP_CHECKF_H
+#define EXAMPLE_NNP_CHECKF_H
+
+#include "Example_nnp.h"
+#include "BoostDataContainer.h"
+
+struct Example_nnp_checkf : public Example_nnp
+{
+    Example_nnp_checkf(std::string name)
+        : Example_nnp("nnp-checkf", name) {};
+};
+
+template<>
+void BoostDataContainer<Example_nnp_checkf>::setup()
+{
+    Example_nnp_checkf* e = nullptr;
+
+    examples.push_back(Example_nnp_checkf("H2O_RPBE-D3"));
+    e = &(examples.back());
+    e->args = "";
+
+    examples.push_back(Example_nnp_checkf("LJ"));
+    e = &(examples.back());
+    e->args = "";
+
+    return;
+}
+
+#endif

test/cpp/test_nnp-checkf.cpp

@@ -0,0 +1,23 @@
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE nnp-checkf
+#include "Example_nnp_checkf.h"
+#include "nnp_test.h"
+
+#include <limits> // std::numeric_limits
+
+using namespace std;
+
+double const accuracy = 10.0 * numeric_limits<double>::epsilon();
+
+BoostDataContainer<Example_nnp_checkf> container;
+
+NNP_TOOL_TEST_CASE()
+
+void nnpToolTestBody(Example_nnp_checkf const /*example*/)
+{
+    BOOST_REQUIRE(bfs::exists("nnp-checkf.log.0000"));
+    BOOST_REQUIRE(bfs::exists("checkf-forces.out"));
+    BOOST_REQUIRE(bfs::exists("checkf-summary.out"));
+
+    return;
+}