Changeset 26062f

Timestamp:

Apr 23, 2021, 8:31:23 PM (5 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, Candidate_v1.7.1, stable

Children:

cbbb6a

Parents:

b56827

git-author:

Frederik Heber <frederik.heber@…> (04/22/19 23:01:18)

git-committer:

Frederik Heber <frederik.heber@…> (04/23/21 20:31:23)

Message:

StoreSaturatedFragmentAction may now export to FragmentQueue as well.

• DOCU: Added explanation about adding to FragmentQueue.

Files:

• doc/userguide/userguide.xml (modified) (1 diff)
• src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) (3 diffs)
• src/Actions/FragmentationAction/StoreSaturatedFragmentAction.def (modified) (2 diffs)

doc/userguide/userguide.xml

@@ -2083 +2083 @@
           where all dangling bonds (by atoms that are connected in the bond
           graph but have not been selected as well) are saturated with
-          additional hydrogen atoms. The output formats are set to just xyz.
-          </para>
+          additional hydrogen atoms.</para>
+          <para>This can work two ways: Either the saturated fragment is 
+          written to file. If not "output-types" is given, then the fragment
+          will instead be written to the FragmentQueue. In other words, its
+          energy is calculated when <link linkend="fragmentation.fragment-automation">fragment automation</link> is used.</para>
           <programlisting>
   ... --store-saturated-fragment \
       --DoSaturate 1 \
       --output-types xyz
+          </programlisting>
+          <para>Alternatively, use the following to store in fragment job 
+          queue.</para>
+          <programlisting>
+  ... --store-saturated-fragment \
+      --DoSaturate 1 \
+      --grid-level 6
+      --max_meshwidth 0.3
        </programlisting>
         </section>

src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp

@@ -3 +3 @@
  * Description: creates and alters molecular systems
  * Copyright (C)  2013 University of Bonn. All rights reserved.
- * Copyright (C)  2013 Frederik Heber. All rights reserved.
+ * Copyright (C)  2013-2019 Frederik Heber. All rights reserved.
  * 
  *
@@ -39 +39 @@
 #include "CodePatterns/Log.hpp"
 #include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
+#include "Fragmentation/Exporters/ExportGraph_ToJobs.hpp"
 #include "Fragmentation/Exporters/SaturatedFragment.hpp"
 #include "Fragmentation/Graph.hpp"
@@ -82 +83 @@
 
     const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
-    ExportGraph_ToFiles exporter(TotalGraph, IncludeHydrogen, saturation, globalsaturationpositions);
-    exporter.setPrefix(params.prefix.get());
-    exporter.setOutputTypes(params.types.get());
-    exporter();
+    if (params.types.get().size() != 0) {
+      // store molecule's fragment to file
+      ExportGraph_ToFiles exporter(TotalGraph, IncludeHydrogen, saturation, globalsaturationpositions);
+      exporter.setPrefix(params.prefix.get());
+      exporter.setOutputTypes(params.types.get());
+      if (!exporter())
+        return Action::failure;
+    } else {
+      // store molecule's fragment in FragmentJobQueue
+      ExportGraph_ToJobs exporter(TotalGraph, IncludeHydrogen, saturation, globalsaturationpositions);
+      exporter.setLevel(params.level.get());
+      exporter.setMaximumMeshWidth(params.max_meshwidth.get());
+      if (!exporter())
+        return Action::failure;
+    }
   }
 

src/Actions/FragmentationAction/StoreSaturatedFragmentAction.def

@@ -11 +11 @@
 
 #include "Parameters/Validators/DummyValidator.hpp"
+#include "Parameters/Validators/RangeValidator.hpp"
 #include "Parameters/Validators/STLVectorValidator.hpp"
+#include "Parameters/Validators/Specific/BoxLengthValidator.hpp"
 #include "Parameters/Validators/Specific/ParserTypeValidator.hpp"
 
@@ -17 +19 @@
 // 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)(bool)(std::vector<std::string>)
-#define paramtokens ("store-saturated-fragment")("DoSaturate")("output-types")
-#define paramdescriptions ("name of fragment file")("do saturate dangling bonds with hydrogen")("type(s) of parsers that output fragment config files")
-#define paramdefaults (NOPARAM_DEFAULT)(PARAM_DEFAULT(true))(PARAM_DEFAULT(std::vector<std::string>()))
-#define paramreferences (prefix)(DoSaturation)(types)
+#define paramtypes (std::string)(bool)(std::vector<std::string>)(double)(unsigned int)
+#define paramtokens ("store-saturated-fragment")("DoSaturate")("output-types")("max-meshwidth")("grid-level")
+#define paramdescriptions ("name of fragment file")("do saturate dangling bonds with hydrogen")("type(s) of parsers that output fragment config files")("maximum allowed mesh width, i.e. discrete points may be at most that far apart on the fragment grids")("resolution of density sampling multigrid")
+#define paramdefaults (NOPARAM_DEFAULT)(PARAM_DEFAULT(true))(PARAM_DEFAULT(std::vector<std::string>()))(PARAM_DEFAULT(0.))(PARAM_DEFAULT(5))
+#define paramreferences (prefix)(DoSaturation)(types)(max_meshwidth)(level)
 #define paramvalids \
 (DummyValidator< std::string >()) \
 (DummyValidator< bool >()) \
-(STLVectorValidator< std::vector<std::string> >(1, 10, ParserTypeValidator()))
+(STLVectorValidator< std::vector<std::string> >(0, 10, ParserTypeValidator())) \
+(BoxLengthValidator()) \
+(RangeValidator< unsigned int >(1, 10))
 
 #undef statetypes