Changeset 9b0dcd

Timestamp:

May 19, 2021, 7:06:29 PM (4 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

20fc6f

Parents:

c98620

git-author:

Frederik Heber <frederik.heber@…> (05/19/21 19:03:24)

git-committer:

Frederik Heber <frederik.heber@…> (05/19/21 19:06:29)

Message:

Added potential-list argument to GeneratePotentialsAction.

• DOCU: Extended documentation on new option.
• TEST: Added a test case on this.

Files:

• doc/userguide/userguide.xml (modified) (2 diffs)
• src/Actions/PotentialAction/GeneratePotentialsAction.cpp (modified) (4 diffs)
• src/Actions/PotentialAction/GeneratePotentialsAction.def (modified) (1 diff)
• tests/Python/AllActions/options.dat (modified) (1 diff)
• tests/regression/Potential/GeneratePotentials/post/water_restricted.potentials (added)
• tests/regression/Potential/GeneratePotentials/testsuite-potential-generate-potentials.at (modified) (1 diff)

doc/userguide/userguide.xml

@@ -2470 +2470 @@
           particle types the following action can be called:
           <programlisting>
-                  ... --generate-potentials
+                  ... --generate-potentials \
                   --fragment-charges 8 1 1
           </programlisting>
@@ -2478 +2478 @@
           subgraphs do not exists for the molecule H-O-H), and tersoff for the
           types O and H.
-        </para>
+          <programlisting>
+                  ... --generate-potentials \
+                  --fragment-charges 8 1 1 \
+                  --potential-list constant harmonic_bond harmonic_angle
+          </programlisting>
+          This would generate the potentials taken from the restricted set of 
+          listed potential names. If the give list is empty (i.e. the parameter
+          is unset), then by default all available potentials are used.</para>
         </section>
         <section xml:id="potentials.save-potential">

src/Actions/PotentialAction/GeneratePotentialsAction.cpp

@@ -43 +43 @@
 #include <string>
 
+#include <boost/foreach.hpp>
+
 #include "Actions/PotentialAction/GeneratePotentialsAction.hpp"
 
@@ -80 +82 @@
   }
 
+  // gather list of potential candidates
+  std::vector<std::string> potentials;
+  if (!params.potential_list.isSet()) {
+    for (unsigned int i=0; i<PotentialTypesMax; ++i)
+      potentials.push_back(PotentialFactory::getNameForType((enum PotentialTypes)i));
+  } else
+    potentials = params.potential_list.get();
+
   // go through all potential potentials :)4
   const PotentialFactory& factory = PotentialFactory::getConstInstance();
@@ -86 +96 @@
   typedef std::set<BindingModel> unique_models_t;
   unique_models_t unique_models;
-  for (unsigned int i=0; i<PotentialTypesMax; ++i) {
-    const std::string potential_name = PotentialFactory::getNameForType((enum PotentialTypes)i);
+  BOOST_FOREACH(std::string &potential_name, potentials) {
     unique_models.clear();
 
@@ -102 +111 @@
 
     // first need to construct potential, then may access it
-    EmpiricalPotential const * const defaultPotential = factory.getDefaultPotential((enum PotentialTypes)i);
+    const enum PotentialTypes potential_type = factory.getTypeForName(potential_name);
+    EmpiricalPotential const * const defaultPotential = factory.getDefaultPotential(potential_type);
     /// 1. get its number of particles
     const unsigned int num_particles = defaultPotential->getParticleTypeNumber();

src/Actions/PotentialAction/GeneratePotentialsAction.def

@@ -9 +9 @@
 #include "Parameters/Validators/STLVectorValidator.hpp"
 #include "Parameters/Validators/Specific/ElementValidator.hpp"
+#include "Parameters/Validators/Specific/PotentialTypeValidator.hpp"
+#include <string>
+#include <vector>
 
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (std::vector<const element *>)
-#define paramtokens ("fragment-charges")
-#define paramdescriptions ("charges specifying the fragment")
-#define paramdefaults (NOPARAM_DEFAULT)
-#define paramreferences (fragment)
+#define paramtypes (std::vector<const element *>)(std::vector<std::string>)
+#define paramtokens ("fragment-charges")("potential-list")
+#define paramdescriptions ("charges specifying the fragment")("list of potentials to generate or empty for all")
+#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)
+#define paramreferences (fragment)(potential_list)
 #define paramvalids \
-(STLVectorValidator< std::vector<const element *> >(0,99, ElementValidator()))
+(STLVectorValidator< std::vector<const element *> >(0,99, ElementValidator())) \
+(STLVectorValidator< std::vector<std::string> >(0,99, PotentialTypeValidator()))
 
 #undef statetypes

tests/Python/AllActions/options.dat

@@ -161 +161 @@
 potential_charges       "1 1"
 potential_type  "morse"
+potential_list  "angle harmonic_bond"
 radius  "20."
 random_atom_displacement        "0."

tests/regression/Potential/GeneratePotentials/testsuite-potential-generate-potentials.at

@@ -32 +32 @@
 
 AT_CLEANUP
+
+AT_SETUP([Potential - generate potentials for water, restricted set])
+AT_KEYWORDS([potential parse-homologies generate-potentials water])
+
+file=water_homologies.dat
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/GeneratePotentials/pre/$file $file], 0)
+AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder \
+        --parse-homologies $file \
+        --generate-potentials \
+                --fragment-charges 1 8 1 \
+                --potential-list constant harmonic_bond harmonic_angle \
+        --save-potentials water.potentials], 0, [stdout], [ignore])
+AT_CHECK([diff water.potentials ${abs_top_srcdir}/tests/regression/Potential/GeneratePotentials/post/water_restricted.potentials], 0, [ignore], [ignore])
+
+AT_CLEANUP