v13.2.0 fixes for VASP ML output handling, queueRefreshInterval update in runtime

Author: hajinazar

CMakeLists.txt

@@ -2,8 +2,8 @@ cmake_minimum_required(VERSION 3.0...3.27)
 project(XtalOpt)
 
 set(XtalOpt_VERSION_MAJOR 13)
-set(XtalOpt_VERSION_MINOR 1)
-set(XtalOpt_VERSION_PATCH 1)
+set(XtalOpt_VERSION_MINOR 2)
+set(XtalOpt_VERSION_PATCH 0)
 set(XtalOpt_VERSION "${XtalOpt_VERSION_MAJOR}.${XtalOpt_VERSION_MINOR}")
 set(XtalOpt_VERSION_FULL "${XtalOpt_VERSION}.${XtalOpt_VERSION_PATCH}")
 

src/globalsearch/constants.h

@@ -1,3 +1,18 @@
+/**********************************************************************
+  constants.h - Constants and conversion factors used in XtalOpt.
+
+  Copyright (C) 2024 by Samad Hajinazar
+
+  This source code is released under the New BSD License, (the "License").
+
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+
+ ***********************************************************************/
+
 #ifndef CONSTANTS_H
 #define CONSTANTS_H
 

src/globalsearch/formats/poscarformat.cpp

@@ -101,8 +101,12 @@ bool PoscarFormat::read(Structure& s, std::istream& in)
     // Assume atomic symbols are here and store them
     symbolsList = split(line, ' ');
     // Store atomic nums
-    for (size_t i = 0; i < symbolsList.size(); ++i)
-      atomicNumbers.push_back(ElemInfo::getAtomicNum(symbolsList[i]));
+    for (size_t i = 0; i < symbolsList.size(); ++i) {
+      // This is to handle VASP compiled with HDF5 where "/..."
+      //   might appear after species symbol
+      string sptype = symbolsList[i].substr(0, symbolsList[i].find("/"));
+      atomicNumbers.push_back(ElemInfo::getAtomicNum(sptype));
+    }
     // This next one should be atom types
     getline(in, line);
   }
@@ -119,8 +123,12 @@ bool PoscarFormat::read(Structure& s, std::istream& in)
       }
       // Now get the symbols with a simple space split
       symbolsList = split(trimFormula, ' ');
-      for (size_t i = 0; i < symbolsList.size(); ++i)
-        atomicNumbers.push_back(ElemInfo::getAtomicNum(symbolsList.at(i)));
+      for (size_t i = 0; i < symbolsList.size(); ++i) {
+        // This is to handle VASP compiled with HDF5 where "/..."
+        //   might appear after species symbol
+        string sptype = symbolsList[i].substr(0, symbolsList[i].find("/"));
+        atomicNumbers.push_back(ElemInfo::getAtomicNum(sptype));
+      }
     }
   }
 

src/globalsearch/formats/vaspformat.cpp

@@ -123,15 +123,15 @@ bool VaspFormat::getOUTCAREnthalpy(std::istream& in, double& enthalpy)
   in.seekg(0, std::ios::end);
   while (in.tellg() >= 0) {
     reverseGetline(in, line);
-    if (strstr(line.c_str(), "enthalpy is")) {
+    if (strstr(line.c_str(), "enthalpy is  TOTEN")) {
       vector<string> stringSplit = split(line, ' ');
       // Make sure the line is long enough. If not, just keep reading.
       if (stringSplit.size() < 5)
         continue;
 
       enthalpy = atof(stringSplit[4].c_str());
       return true;
-    } else if (strstr(line.c_str(), "enthalpy is ML")) { // VASP ML output
+    } else if (strstr(line.c_str(), "enthalpy is ML TOTEN")) { // VASP ML output
       vector<string> stringSplit = split(line, ' ');
       // Make sure the line is long enough. If not, just keep reading.
       if (stringSplit.size() < 6)

src/xtalopt/cliOptions.cpp

@@ -1416,6 +1416,8 @@ void XtalOptCLIOptions::writeInitialRuntimeFile(XtalOpt& xtalopt)
     QString("spglibTolerance = ") + QString::number(xtalopt.tol_spg) + "\n";
 
   text += QString("\n# Queue Interface Settings\n");
+  text += QString("queueRefreshInterval = ") +
+          QString::number(xtalopt.queueRefreshInterval()) + "\n";
   text += QString("autoCancelJobAfterTime = ") +
           fromBool(xtalopt.m_cancelJobAfterTime) + "\n";
 
@@ -1609,6 +1611,8 @@ void XtalOptCLIOptions::processRuntimeOptions(
       xtalopt.m_cancelJobAfterTime = toBool(options[option]);
     } else if (CICompare("hoursForAutoCancelJob", option)) {
       xtalopt.m_hoursForCancelJobAfterTime = options[option].toDouble();
+    } else if (CICompare("queueRefreshInterval", option)) {
+      xtalopt.setQueueRefreshInterval(options[option].toUInt());
     } else if (CICompare("softExit", option)) {
       xtalopt.m_softExit = toBool(options[option]);
     } else if (CICompare("hardExit", option)) {