Changeset 56c55f3

Timestamp:

Aug 31, 2016, 10:54:47 AM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

FragmentMolecule_checks_bonddegrees, Gui_Fixes

Children:

e3d0fe

Parents:

6e5ca9

git-author:

Frederik Heber <heber@…> (08/31/16 10:45:35)

git-committer:

Frederik Heber <heber@…> (08/31/16 10:54:47)

Message:

Added "parse-state-files" option to fragment-molecule which is off by default.

• this prevents accidental parsing of stale keysets, adjacency, or orderatsite files. These hard to find errors ever and again cause failing fragmentation because e.g. some hydrogen is suddenly in the keysets although hydrogens are excluded.

Files:

• src/Actions/FragmentationAction/FragmentationAction.cpp (modified) (4 diffs)
• src/Actions/FragmentationAction/FragmentationAction.def (modified) (2 diffs)
• src/Fragmentation/Fragmentation.cpp (modified) (2 diffs)
• src/Fragmentation/Fragmentation.hpp (modified) (1 diff)
• tests/Python/AllActions/options.dat (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -41 +41 @@
 #include "Descriptors/AtomSelectionDescriptor.hpp"
 #include "Descriptors/MoleculeIdDescriptor.hpp"
+#include "Fragmentation/AdaptivityMap.hpp"
 #include "Fragmentation/Exporters/ExportGraph_ToAtomFragments.hpp"
 #include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
@@ -117 +118 @@
   boost::shared_ptr<AdjacencyList> FileChecker;
   boost::filesystem::path filename(params.prefix.get() + std::string(ADJACENCYFILE));
-  if (boost::filesystem::exists(filename) && boost::filesystem::is_regular_file(filename)) {
+  if ((params.ParseStateFiles.get())
+    && boost::filesystem::exists(filename)
+    && boost::filesystem::is_regular_file(filename)) {
     std::ifstream File;
     File.open(filename.string().c_str(), ios::out);
@@ -144 +147 @@
   // we parse in the keysets from last time if present
   Graph StoredGraph;
-  StoredGraph.ParseKeySetFile(params.prefix.get());
+  if (params.ParseStateFiles.get()) {
+    StoredGraph.ParseKeySetFile(params.prefix.get());
+    // check parsed graph against the set of atoms
+    {
+      AdaptivityMap *amap = StoredGraph.GraphToAdaptivityMap();
+      bool status = true;
+      for (World::AtomSelectionConstIterator iter = world.beginAtomSelection();
+          iter != world.endAtomSelection(); ++iter) {
+        const atomId_t atomid = iter->second->getId();
+        // skip hydrogens in check if saturation is turned on
+        if ((iter->second->getType()->getAtomicNumber() != 1)
+            || (!params.DoSaturation.get())) {
+          if (amap->count(atomid) == 0) {
+            ELOG(1, "Atom #" << atomid << " not contained in KeySet file. ");
+            status = false;
+            break;
+          }
+        } else if (amap->count(atomid) != 0) {
+          ELOG(1, "Atom #" << atomid << " in KeySet file is a hydrogen, but is now excluded. ");
+          status = false;
+          break;
+        }
+      }
+      delete amap;
+
+      if (!status) {
+        ELOG(1, "KeySetsFile seems to contain leftover from an old fragmentation, hence not using file.");
+        StoredGraph.clear();
+      }
+    }
+  }
 
   start = clock();
@@ -174 +207 @@
     {
       Graph StoredLocalGraph(StoredGraph.getLocalGraph(mol));
-      const int tempFlag = Fragmenter.FragmentMolecule(mols_atomids, params.order.get(), params.prefix.get(), StoredLocalGraph);
+      const int tempFlag = Fragmenter.FragmentMolecule(mols_atomids, params.order.get(), params.prefix.get(), StoredLocalGraph, params.ParseStateFiles.get());
       if ((ExitFlag == 2) && (tempFlag != 2))
         ExitFlag = tempFlag; // if there is one molecule that needs further fragmentation, it overrides others

src/Actions/FragmentationAction/FragmentationAction.def

@@ -21 +21 @@
 // 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::string)(double)(int)(bool)(bool)(std::vector<std::string>)(unsigned int)(unsigned int)(bool)
-#define paramtokens ("fragment-molecule")("distance")("order")("DoSaturate")("ExcludeHydrogen")("output-types")("grid-level")("inter-order")("DoCyclesFull")
-#define paramdescriptions ("prefix of each fragment file")("distance in space up to which fragments are combined")("order of a discretization, dissection, ...")("do saturate dangling bonds with hydrogen")("whether to exclude hydrogen in the bond graph dissection or not")("type(s) of parsers that output fragment config files")("resolution of density sampling multigrid")("up to which order distinct fragments are combined")("always calculate (aromatic) rings fully, even beyond desired order")
-#define paramdefaults (PARAM_DEFAULT("BondFragment"))(PARAM_DEFAULT(3.))(PARAM_DEFAULT(3))(PARAM_DEFAULT(true))(PARAM_DEFAULT(true))(NOPARAM_DEFAULT)(PARAM_DEFAULT(5))(PARAM_DEFAULT(0))(PARAM_DEFAULT(false))
-#define paramreferences (prefix)(distance)(order)(DoSaturation)(HowtoTreatHydrogen)(types)(level)(InterOrder)(DoCyclesFull)
+#define paramtypes (std::string)(double)(int)(bool)(bool)(std::vector<std::string>)(unsigned int)(unsigned int)(bool)(bool)
+#define paramtokens ("fragment-molecule")("distance")("order")("DoSaturate")("ExcludeHydrogen")("output-types")("grid-level")("inter-order")("DoCyclesFull")("parse-state-files")
+#define paramdescriptions ("prefix of each fragment file")("distance in space up to which fragments are combined")("order of a discretization, dissection, ...")("do saturate dangling bonds with hydrogen")("whether to exclude hydrogen in the bond graph dissection or not")("type(s) of parsers that output fragment config files")("resolution of density sampling multigrid")("up to which order distinct fragments are combined")("always calculate (aromatic) rings fully, even beyond desired order")("whether to parse keysets, orderatsite, adjacency from state files")
+#define paramdefaults (PARAM_DEFAULT("BondFragment"))(PARAM_DEFAULT(3.))(PARAM_DEFAULT(3))(PARAM_DEFAULT(true))(PARAM_DEFAULT(true))(NOPARAM_DEFAULT)(PARAM_DEFAULT(5))(PARAM_DEFAULT(0))(PARAM_DEFAULT(false))(PARAM_DEFAULT(false))
+#define paramreferences (prefix)(distance)(order)(DoSaturation)(HowtoTreatHydrogen)(types)(level)(InterOrder)(DoCyclesFull)(ParseStateFiles)
 #define paramvalids \
 (DummyValidator< std::string >()) \
@@ -35 +35 @@
 (RangeValidator< unsigned int >(1, 10)) \
 (DummyValidator< unsigned int >()) \
+(DummyValidator< bool >()) \
 (DummyValidator< bool >())
 

src/Fragmentation/Fragmentation.cpp

@@ -118 +118 @@
     int Order,
     const std::string &prefix,
-    const Graph &ParsedFragmentList)
+    const Graph &ParsedFragmentList,
+    const bool _ParseStateFile)
 {
   std::fstream File;
@@ -178 +179 @@
 
   // ===== 4. check globally whether there's something to do actually (first adaptivity check)
-  FragmentationToDo = FragmentationToDo && ParseOrderAtSiteFromFile(atomids, prefix, Global_local_bimap);
+  if (_ParseStateFile)
+    FragmentationToDo = FragmentationToDo && ParseOrderAtSiteFromFile(atomids, prefix, Global_local_bimap);
 
   // =================================== Begin of FRAGMENTATION ===============================

src/Fragmentation/Fragmentation.hpp

@@ -46 +46 @@
   ~Fragmentation();
 
-  int FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, const std::string &prefix, const Graph &ParsedFragmentList);
+  int FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, const std::string &prefix, const Graph &ParsedFragmentList, const bool _ParseStateFile);
 
   const Graph& getGraph() const {

tests/Python/AllActions/options.dat

@@ -132 +132 @@
 parse-particle-parameters       "water.particles"
 parse-potentials        "water.potentials"
+parse-state-files       "1"
 parse-tremolo-potentials        "argon.potentials"
 parse-tremolo-potentials        "tensid.potentials"