Merge pull request #111 from OpenBioSim/feature_bond_breaking

Feature bond breaking
OpenBioSim · Oct 10, 2023 · 9e4edb8 · 9e4edb8
2 parents 1d1c97f + 7599bba
commit 9e4edb8
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diff --git a/README.rst b/README.rst
@@ -45,15 +45,15 @@ To create a new environment:
 
     mamba create -n openbiosim "python<3.11"
     mamba activate openbiosim
-    mamba install -c openbiosim sire
+    mamba install -c conda-forge -c openbiosim sire
 
 To install the latest development version you can use:
 
 .. code-block:: bash
 
     mamba create -n openbiosim-dev "python<3.11"
     mamba activate openbiosim-dev
-    mamba install -c openbiosim/label/dev sire
+    mamba install -c conda-forge -c openbiosim/label/dev sire
 
 However, as you are here, it is likely you want to download the latest,
 greatest version of the code, which you will need to compile. To compile

diff --git a/corelib/src/libs/SireCAS/lambdaschedule.cpp b/corelib/src/libs/SireCAS/lambdaschedule.cpp
@@ -432,14 +432,23 @@ void LambdaSchedule::clear()
     this->constant_values = Values();
 }
 
+/** Append a morph stage onto this schedule. The morph stage is a
+ *  standard stage that scales each forcefield parameter by
+ *  (1-:lambda:).initial + :lambda:.final
+ */
+void LambdaSchedule::addMorphStage(const QString &name)
+{
+    this->addStage(name, (this->lam() * this->final()) +
+                             ((1 - this->lam()) * this->initial()));
+}
+
 /** Append a morph stage onto this schedule. The morph stage is a
  *  standard stage that scales each forcefield parameter by
  *  (1-:lambda:).initial + :lambda:.final
  */
 void LambdaSchedule::addMorphStage()
 {
-    this->addStage("morph", (this->lam() * this->final()) +
-                                ((1 - this->lam()) * this->initial()));
+    this->addMorphStage("morph");
 }
 
 /** Sandwich the current set of stages with a charge-descaling and
@@ -450,7 +459,9 @@ void LambdaSchedule::addMorphStage()
  *  by :gamma:. A final charge-rescaling stage is then appended that
  *  scales the charge parameter from :gamma:.final to final.
  */
-void LambdaSchedule::addChargeScaleStages(double scale)
+void LambdaSchedule::addChargeScaleStages(const QString &decharge_name,
+                                          const QString &recharge_name,
+                                          double scale)
 {
     auto scl = this->setConstant("γ", scale);
 
@@ -462,11 +473,24 @@ void LambdaSchedule::addChargeScaleStages(double scale)
     }
 
     // now prepend the decharging stage, and append the recharging stage
-    this->prependStage("decharge", this->initial());
-    this->appendStage("recharge", this->final());
+    this->prependStage(decharge_name, this->initial());
+    this->appendStage(recharge_name, this->final());
+
+    this->setEquation(decharge_name, "charge", (1.0 - ((1.0 - scl) * this->lam())) * this->initial());
+    this->setEquation(recharge_name, "charge", (1.0 - ((1.0 - scl) * (1.0 - this->lam()))) * this->final());
+}
 
-    this->setEquation("decharge", "charge", (1.0 - ((1.0 - scl) * this->lam())) * this->initial());
-    this->setEquation("recharge", "charge", (1.0 - ((1.0 - scl) * (1.0 - this->lam()))) * this->final());
+/** Sandwich the current set of stages with a charge-descaling and
+ *  a charge-scaling stage. This prepends a charge-descaling stage
+ *  that scales the charge parameter down from `initial` to
+ *  :gamma:.initial (where :gamma:=`scale`). The charge parameter in all of
+ *  the exising stages in this schedule are then multiplied
+ *  by :gamma:. A final charge-rescaling stage is then appended that
+ *  scales the charge parameter from :gamma:.final to final.
+ */
+void LambdaSchedule::addChargeScaleStages(double scale)
+{
+    this->addChargeScaleStages("decharge", "recharge", scale);
 }
 
 /** Prepend a stage called 'name' which uses the passed 'equation'

diff --git a/corelib/src/libs/SireCAS/lambdaschedule.h b/corelib/src/libs/SireCAS/lambdaschedule.h
@@ -117,7 +117,12 @@ namespace SireCAS
                          const SireCAS::Expression &equation);
 
         void addMorphStage();
+        void addMorphStage(const QString &name);
+
         void addChargeScaleStages(double scale = 0.2);
+        void addChargeScaleStages(const QString &decharge_name,
+                                  const QString &recharge_name,
+                                  double scale = 0.2);
 
         void setEquation(const QString &stage,
                          const QString &lever,

diff --git a/corelib/src/libs/SireIO/moleculeparser.cpp b/corelib/src/libs/SireIO/moleculeparser.cpp
@@ -2323,17 +2323,24 @@ QStringList MoleculeParser::write(const System &system, const QString &filename,
     QStringList filenames;
     QStringList fileformats;
 
-    const auto format_property = map["fileformat"];
-
-    if (format_property.hasValue())
+    if (map.specified("fileformat"))
     {
-        try
+        const auto format_property = map["fileformat"];
+
+        if (format_property.hasSource())
         {
-            fileformats = format_property.value().asA<StringProperty>().toString().split(",");
+            fileformats = format_property.source().split(",");
         }
-        catch (...)
+        else
         {
-            fileformats.append(format_property.value().asA<MoleculeParser>().formatName());
+            try
+            {
+                fileformats = format_property.value().asA<StringProperty>().toString().split(",");
+            }
+            catch (...)
+            {
+                fileformats.append(format_property.value().asA<MoleculeParser>().formatName());
+            }
         }
 
         const auto fileinfo = QFileInfo(filename);
@@ -2353,7 +2360,7 @@ QStringList MoleculeParser::write(const System &system, const QString &filename,
             // we need to find the format from the system
             try
             {
-                fileformats = system.property(format_property).asA<StringProperty>().toString().split(",");
+                fileformats = system.property(map["fileformat"]).asA<StringProperty>().toString().split(",");
             }
             catch (...)
             {
@@ -2404,17 +2411,24 @@ QStringList MoleculeParser::write(const System &system, const QStringList &files
     QStringList filenames;
     QStringList fileformats;
 
-    const auto format_property = map["fileformat"];
-
-    if (format_property.hasValue())
+    if (map.specified("fileformat"))
     {
-        try
+        const auto format_property = map["fileformat"];
+
+        if (format_property.hasSource())
         {
-            fileformats = format_property.value().asA<StringProperty>().toString().split(",");
+            fileformats = format_property.source().split(",");
         }
-        catch (...)
+        else
         {
-            fileformats.append(format_property.value().asA<MoleculeParser>().formatName());
+            try
+            {
+                fileformats = format_property.value().asA<StringProperty>().toString().split(",");
+            }
+            catch (...)
+            {
+                fileformats.append(format_property.value().asA<MoleculeParser>().formatName());
+            }
         }
 
         if (files.count() != fileformats.count())
@@ -2449,7 +2463,7 @@ QStringList MoleculeParser::write(const System &system, const QStringList &files
         // we may need to find the format from the system
         try
         {
-            fileformats = system.property(format_property).asA<StringProperty>().toString().split(",");
+            fileformats = system.property(map["fileformat"]).asA<StringProperty>().toString().split(",");
         }
         catch (...)
         {