Parse inputParameters if present in cjson (#1849)

* Parse inputParameters if present in cjson and use in input generators Signed-off-by: Geoff Hutchison <[email protected]> --------- Signed-off-by: Geoff Hutchison <[email protected]>
OpenChemistry · Dec 8, 2024 · e550046 · e550046
1 parent 6baaa03
commit e550046
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Showing 2 changed files with 46 additions and 1 deletion.
diff --git a/avogadro/io/cjsonformat.cpp b/avogadro/io/cjsonformat.cpp
@@ -677,6 +677,13 @@ bool CjsonFormat::deserialize(std::istream& file, Molecule& molecule,
     }
   }
 
+  // inputParameters are calculation metadata
+  if (jsonRoot.find("inputParameters") != jsonRoot.end()) {
+    json inputParameters = jsonRoot["inputParameters"];
+    // add this as a string to the molecule data
+    molecule.setData("inputParameters", inputParameters.dump());
+  }
+
   // Partial charges are optional, but if present should be loaded.
   json partialCharges = atoms["partialCharges"];
   if (partialCharges.is_object()) {
@@ -763,6 +770,13 @@ bool CjsonFormat::serialize(std::ostream& file, const Molecule& molecule,
     if (element.first == "name" || element.first == "inchi")
       continue;
 
+    // check for "inputParameters" and handle it separately
+    if (element.first == "inputParameters") {
+      json inputParameters = json::parse(element.second.toString());
+      root["inputParameters"] = inputParameters;
+      continue;
+    }
+
     if (element.second.type() == Variant::String)
       properties[element.first] = element.second.toString().c_str();
     else if (element.second.type() == Variant::Double)
@@ -773,7 +787,15 @@ bool CjsonFormat::serialize(std::ostream& file, const Molecule& molecule,
       properties[element.first] = element.second.toInt();
     else if (element.second.type() == Variant::Bool)
       properties[element.first] = element.second.toBool();
-    else if (element.second.type() == Variant::Matrix) {
+    else if (element.second.type() == Variant::Vector) {
+      // e.g. dipole moment
+      Vector3 v = element.second.toVector3();
+      json vector;
+      vector.push_back(v.x());
+      vector.push_back(v.y());
+      vector.push_back(v.z());
+      properties[element.first] = vector;
+    } else if (element.second.type() == Variant::Matrix) {
       MatrixX m = element.second.toMatrix();
       json matrix;
       for (int i = 0; i < m.rows(); ++i) {
@@ -820,6 +842,7 @@ bool CjsonFormat::serialize(std::ostream& file, const Molecule& molecule,
   }
 
   // check for spectra data
+  // vibrations are separate
   if (molecule.spectraTypes().size() != 0) {
     json spectra, electronic, nmr;
     bool hasElectronic = false;

diff --git a/avogadro/qtgui/jsonwidget.cpp b/avogadro/qtgui/jsonwidget.cpp
@@ -47,6 +47,28 @@ void JsonWidget::setMolecule(QtGui::Molecule* mol)
 
     setOption("Charge", charge);
     setOption("Multiplicity", multiplicity);
+
+    // check the molecule for "inputParameters" from CJSON
+    // e.g.
+    // https://github.com/OpenChemistry/chemicaljson/blob/main/chemicaljson.py#L130
+    if (m_molecule->hasData("inputParameters")) {
+      QByteArray data(m_molecule->data("inputParameters").toString().c_str());
+      QJsonDocument doc = QJsonDocument::fromJson(data);
+      if (!doc.isNull() && doc.isObject()) {
+        QJsonObject inputParameters = doc.object();
+        // check for a few known keys
+        if (inputParameters.contains("processors"))
+          setOption("Processor Cores", inputParameters["processors"].toInt());
+        else if (inputParameters.contains("memory"))
+          setOption("Memory", inputParameters["memory"].toInt());
+        else if (inputParameters.contains("basis"))
+          setOption("Basis", inputParameters["basis"].toString());
+        else if (inputParameters.contains("functional"))
+          setOption("Theory", inputParameters["functional"].toString());
+        else if (inputParameters.contains("task"))
+          setOption("Calculation Type", inputParameters["task"].toString());
+      }
+    }
   }
 
   if (mol == m_molecule)