v13.1.0 seedStructures in CLI; fixed a potential infinite loop in xtal gen; adjusted version variable and docs; removed mol unit leftovers

Author: hajinazar

CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.0...3.27)
 project(XtalOpt)
 
 set(XtalOpt_VERSION_MAJOR 13)
-set(XtalOpt_VERSION_MINOR 0)
+set(XtalOpt_VERSION_MINOR 1)
 set(XtalOpt_VERSION_PATCH 0)
 set(XtalOpt_VERSION "${XtalOpt_VERSION_MAJOR}.${XtalOpt_VERSION_MINOR}")
 set(XtalOpt_VERSION_FULL "${XtalOpt_VERSION}.${XtalOpt_VERSION_PATCH}")
@@ -62,19 +62,6 @@ option( BUILD_TESTS
 if(BUILD_TESTS)
   enable_testing()
 
-  option( RUN_CODE_COV
-  "If this is true, then code coverage will be ran."
-  ON )
-
-  # We will only run codecov stuff on gcc
-  if(CMAKE_COMPILER_IS_GNUCXX AND RUN_CODE_COV)
-    string(CONCAT CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -pedantic -g -O0 "
-                                  "-fprofile-arcs -ftest-coverage")
-    string(CONCAT CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -pedantic -g -O0 "
-                                "-fprofile-arcs -ftest-coverage")
-    string(CONCAT CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} "
-                                         "-fprofile-arcs -ftest-coverage")
-  endif(CMAKE_COMPILER_IS_GNUCXX AND RUN_CODE_COV)
 endif(BUILD_TESTS)
 
 option( ENABLE_SSH

ChangeLog

@@ -1,6 +1,6 @@
 
 ==================================
-========== Release 13.0 ==========
+==========  Release 13  ==========
 ==================================
 
 ===== 0) Highlights
@@ -9,6 +9,7 @@
 0-3)  "Scaled volume" option is added for initiating the minimum and maximum limits of volume per FU
 0-4)  AFLOW-ML entries are removed from CLI and GUI input (it's now a multi-objective objective)
 0-5)  The "old molecular unit" is removed (no ENABLE_MOLECULAR cmake flag and RDKit/Boost dependencies anymore)
+0-6)  Adding seed structures in the CLI mode is supported.
 
 ===== 1) New features, options, outputs, etc.
 1-1)  XtalOpt CLI:
@@ -17,8 +18,10 @@
 - "localQueue" flag for running code locally on a cluster is added for all remote queue types in CLI
 - "softExit" and "hardExit" flags are added for quitting the code in CLI mode
 - Support for "hyphen-separated list of space group numbers" in the CLI input file is added
+- "seedStructures" flag for space-separated list of full path to seed structures is added
 ## Output file:
 - The "opt_step_#" for optimization step is added to "In progress" status in results.txt file
+- Extra Column of "INDX" with the structure index is added to the results.txt file
 1-2)  XtalOpt GUI:
 - "Multiobjective Search" tab is added to GUI, and AFLOW-ML entries are removed from "Search Settings" tab
 - "Plot" tab includes the objective entries in x and y labels, and labeling symbol list
@@ -38,6 +41,7 @@
 2-2)  Fixed the issue of the "Hide" button of the GUI which did nothing or crashed the code on some OS
 2-3)  A potential issue fixed: existence of POTCAR/PSF files was not checked when run started
 2-4)  A potential issue fixed: jobs could fail because of a timing issue in checking the queue
+2-5)  A potential infinite loop in checking suitability of structures for VASP fixed.
 
 ===== 3) Technical and code changes
 3-1)  The remote queues and their use of SSH is re-written
@@ -48,6 +52,7 @@
 fileName->Locpath; filePath->locWorkDir; rempath->remWorkDir
 Some output patterns in *.state files are changed too.
 so, runs performed with older versions can't be resumed unless the *.state files are adjusted.
+3-6)  CMake definition for string variable "XTALOPT_VER" added; to use anywhere inside the code.
 
 ===== 4) Documentation
 4-1)  XtalOpt repo (https://github.com/xtalopt/XtalOpt):
@@ -69,7 +74,7 @@ so, runs performed with older versions can't be resumed unless the *.state files
 
 
 ==================================
-========== Release 12.0 ==========
+==========  Release 12  ==========
 ==================================
 
 ===== 1) New features, options, outputs, etc.
@@ -85,7 +90,7 @@ so, runs performed with older versions can't be resumed unless the *.state files
 
 
 ==================================
-========== Release 11.0 ==========
+==========  Release 11  ==========
 ==================================
 
 ===== 1) New features, options, outputs, etc.
@@ -101,7 +106,7 @@ so, runs performed with older versions can't be resumed unless the *.state files
 
 
 ==================================
-========== Release 10.0 ==========
+==========  Release 10  ==========
 ==================================
 
 ===== 1) New features, options, outputs, etc.
@@ -112,7 +117,7 @@ so, runs performed with older versions can't be resumed unless the *.state files
 
 
 ==================================
-========== Release  9   ==========
+==========  Release  9  ==========
 ==================================
 
 ===== 1) Enhancements / New features:
@@ -150,7 +155,7 @@ by replicating a unit cell to create a supercell for constructing the starting s
 
 
 ==================================
-========== Release  8   ==========
+==========  Release  8  ==========
 ==================================
 
 ===== 1) Enhancements / New features:
@@ -163,7 +168,7 @@ by replicating a unit cell to create a supercell for constructing the starting s
 
 
 ==================================
-========== Release  7   ==========
+==========  Release  7  ==========
 ==================================
 
 ===== 1) Enhancements / New features:
@@ -182,7 +187,7 @@ by replicating a unit cell to create a supercell for constructing the starting s
 
 
 ==================================
-========== Release  6   ==========
+==========  Release  6  ==========
 ==================================
 
 ===== 1) Enhancements / New features:

docs/doxy-api.in

@@ -48,7 +48,7 @@ PROJECT_NAME           = "GlobalSearch API"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "Release 13.0"
+PROJECT_NUMBER         = "Version 13.1"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

docs/doxy-guide.in

@@ -48,7 +48,7 @@ PROJECT_NAME           = "XtalOpt User Guide"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "Release 13.0"
+PROJECT_NUMBER         = "Version 13.1"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

docs/guide/tutorial.dox

@@ -1046,7 +1046,7 @@ the user should provide the following information to the XtalOpt code:
 
    - <b>optimization type:</b> instruction for the code on how to use the result
    of an objective calculation in determining the fitness function.
-   XtalOpt can minimize or maximize a feature, maximize the AFLOW-ML hardness,
+   XtalOpt can minimize or maximize an objective, maximize the AFLOW-ML hardness,
    or use the results of objective calculations for filtering the parents' pool.
    - <b>path to the user-defined script:</b> the full path to the script corresponding to
    the introduced objective. The script will be automatically run by the XtalOpt
@@ -1134,9 +1134,9 @@ can be entered in the corresponding fields by:
  -# choosing the optimization type for the objective from a drop-down menu,
  i.e., "Minimization", "Maximization", "Filtration" (see \ref moes-fil), and
  "Hardness" (see \ref moes-har),
+ -# entering or setting the weight, and
  -# entering the full path to the external code (or script) that calcualtes the objective,
  -# entering the output file name that the external code generates with the objective value,
- -# entering or setting the weight, and
  -# specifying whether a structure discarded by a filtration feature requires further handling or not
  (see \ref moes-fil for more details).
 
@@ -1488,13 +1488,22 @@ and other options may be changed. In addition, if Avogadro2 is open in the
 background and an Avogadro2 RPC server is running, XtalOpt will still also set
 the structure in the Avogadro2 view to the crystals the user selects.
 
+As of XtalOpt version 13, the user can add seed structures in the CLI
+mode as well. This can be done by introducing a "space separated" list of
+full path to the seed structures through the following flag in the XtalOpt input
+file:
+<BR>
+\code
+seedStructures = [path/seed1] [path/seed2] ...
+\endcode
+
 \subsection moes-cli Multiobjective Runs in the XtalOpt CLI
 
 In XtalOpt version 13.0, the multiobjective functionality is implemented,
 as discussed previously in \ref moes section. In order to invoke the multiobjective
-functionality in the CLI mode, for each user-defined feature a line should be added
-to the XtalOpt input file that starts with the keyword features. This line, includes
-the above-mentioned information for the feature and, generally, has the following format:
+functionality in the CLI mode, for each user-defined objective a line should be added
+to the XtalOpt input file that starts with the keyword "objective". This line, includes
+the above-mentioned information for the objective and, generally, has the following format:
 <BR>
 \code
 objective = "optimization_type" "/path_to/script" "script_output_filename" "weight"
@@ -1507,12 +1516,12 @@ It should be noted that in the CLI mode of XtalOpt:
    and only the first three letters are important in identifying the optimization type
    by XtalOpt (i.e., "min", "max", "har", and "fil").
    - Providing the "script output filename" is optional. If this is not specified,
-   the default will be "objective#.out" in which "#" is the number of the feature in the
-   order that it appears in the XtalOpt input file (excluding the "hardness" feature),
+   the default will be "objective#.out" in which "#" is the number of the objective in the
+   order that it appears in the XtalOpt input file (excluding the "hardness" objective),
    e.g., "objective1.out", "objective2.out", etc.
-   - Specifying the "weight" for the feature is optional, as well. If this field is not
-   given for a number of features, it will be determined via the following formula.
-   If any weight is provided for any of the features, it will be subtracted from 1.0 and
+   - Specifying the "weight" for the objective is optional, as well. If this field is not
+   given for a number of objectives, it will be determined via the following formula.
+   If any weight is provided for any of the objectives, it will be subtracted from 1.0 and
    the remaining value will be divided between the enthalpy and objectives that don't have
    a specified weight.
 

src/CMakeLists.txt

@@ -1,3 +1,6 @@
+# String version variable "XTALOPT_VER" for the use anywhere inside the source code
+add_definitions(-DXTALOPT_VER="${XtalOpt_VERSION_MAJOR}.${XtalOpt_VERSION_MINOR}")
+
 add_subdirectory(globalsearch)
 
 if (ENABLE_EXAMPLESEARCH)

src/globalsearch/optbase.h

@@ -483,12 +483,6 @@ class OptBase : public QObject
    */
   void setUsingGUI(bool b) { m_usingGUI = b; }
 
-  /**
-   * Old molecular unit is removed; so always return false for this function
-   */
-  bool molecularMode() { return false; }
-
-
   /**
    * Set the refresh interval for checking remote jobs.
    *

src/xtalopt/cliOptions.cpp

@@ -41,6 +41,7 @@ static const QStringList keywords = { "volumeScaleMin",
                                       "softExit",
                                       "hardExit",
                                       "localQueue",
+                                      "seedStructures",
                                       "empiricalFormula",
                                       "formulaUnits",
                                       "aMin",
@@ -156,7 +157,7 @@ QString XtalOptCLIOptions::xtaloptHeaderString()
 {
   QString out = QString("\n====================================================\n")
               + QString("   XtalOpt Multi-Objective Evolutionary Algorithm   \n")
-              + QString("\n Version %1.%2").arg(XTALOPT_VER_MAJOR).arg(XTALOPT_VER_MINOR)
+              + QString("\n Version %1").arg(XTALOPT_VER)
               + QString("\n Zurek Group, University at Buffalo")
               + QString("\n====================================================\n\n");
   return out;
@@ -350,6 +351,12 @@ bool XtalOptCLIOptions::processOptions(const QHash<QString, QString>& options,
   if (xtalopt.formulaUnitsList.isEmpty())
     xtalopt.formulaUnitsList = { 1 };
 
+  // Seed structures
+  QStringList sl = options.value("seedStructures", "").split(QRegExp("\\s+"), QString::SkipEmptyParts);
+  for (int i = 0; i < sl.size(); i++) {
+    xtalopt.seedList.append(sl.at(i));
+  }
+
   // We put default values in all of these
   // Initialization settings
   xtalopt.a_min = options.value("aMin", "3.0").toFloat();
@@ -376,8 +383,8 @@ bool XtalOptCLIOptions::processOptions(const QHash<QString, QString>& options,
                                  xtalopt.vol_min, xtalopt.vol_max);
   }
 
+  // Check for fixed volume
   if (fabs(xtalopt.vol_min - xtalopt.vol_max) < ZERO5) {
-   // Check for fixed volume
     xtalopt.using_fixed_volume = true;
     xtalopt.vol_fixed = xtalopt.vol_min;
   } else {

src/xtalopt/main.cpp

@@ -66,7 +66,7 @@ int main(int argc, char* argv[])
   QCoreApplication::setOrganizationName("XtalOpt");
   QCoreApplication::setOrganizationDomain("xtalopt.github.io");
   QCoreApplication::setApplicationName("XtalOpt");
-  QCoreApplication::setApplicationVersion(QString("%1.%2").arg(XTALOPT_VER_MAJOR).arg(XTALOPT_VER_MINOR));
+  QCoreApplication::setApplicationVersion(XTALOPT_VER);
 
   QCommandLineParser parser;
   parser.setApplicationDescription("XtalOpt: an open-source multi-objective "

src/xtalopt/xtalopt.cpp

@@ -150,7 +150,7 @@ bool XtalOpt::startSearch()
   }
 
   // Do we have a composition?
-  if (!molecularMode() && comp.isEmpty()) {
+  if (comp.isEmpty()) {
     error("Cannot create structures. Composition is not set.");
     return false;
   }
@@ -269,7 +269,7 @@ bool XtalOpt::startSearch()
   }
 
   // Perform a regular random generation
-  if (!using_randSpg || molecularMode()) {
+  if (!using_randSpg) {
     // Generation loop...
     while (newXtalCount < numInitial) {
       updateProgressBar(numInitial, newXtalCount + failed, newXtalCount);
@@ -1404,7 +1404,14 @@ Xtal* XtalOpt::randSpgXtal(uint generation, uint id, uint FU, uint spg,
 Xtal* XtalOpt::generateEmptyXtalWithLattice(uint FU)
 {
   Xtal* xtal = nullptr;
+  int maxAttempts = 10000;
+  int attemptCount = 0;
   do {
+    if (attemptCount >= maxAttempts) {
+      qDebug() << "Failed too many times in generateEmptyXtalWithLattice. Giving up";
+      return nullptr;
+    }
+    ++attemptCount;
     delete xtal;
     xtal = nullptr;
     double a = getRandDouble() * (a_max - a_min) + a_min;
@@ -1874,7 +1881,7 @@ void XtalOpt::printSubXtal(Xtal* xtal, uint generation, uint id)
 Xtal* XtalOpt::generateRandomXtal(uint generation, uint id)
 {
   QList<uint> tempFormulaUnitsList = formulaUnitsList;
-  if (!molecularMode() && using_mitotic_growth && !using_one_pool) {
+  if (using_mitotic_growth && !using_one_pool) {
     // Remove formula units on the list for which there is a smaller multiple
     // that may be used to create a super cell.
     for (int i = 0; i < tempFormulaUnitsList.size(); i++) {
@@ -3122,7 +3129,7 @@ bool XtalOpt::checkXtal(Xtal* xtal, QString* err)
     return false;
   }
 
-  if (!molecularMode() && !checkComposition(xtal, err))
+  if (!checkComposition(xtal, err))
     return false;
 
   if (!checkLattice(xtal, xtal->getFormulaUnits(), err))
@@ -3149,7 +3156,7 @@ bool XtalOpt::checkXtal(Xtal* xtal, QString* err)
   }
 
   // Check interatomic distances
-  if (using_interatomicDistanceLimit && !molecularMode()) {
+  if (using_interatomicDistanceLimit) {
     int atom1, atom2;
     double IAD;
     if (!xtal->checkInteratomicDistances(this->comp, &atom1, &atom2, &IAD)) {
@@ -3167,7 +3174,7 @@ bool XtalOpt::checkXtal(Xtal* xtal, QString* err)
     }
   }
 
-  if (using_customIAD && !molecularMode()) {
+  if (using_customIAD) {
     int atom1, atom2;
     double IAD;
     if (!xtal->checkMinIAD(this->interComp, &atom1, &atom2, &IAD)) {

src/xtalopt/xtalopt.h

@@ -24,9 +24,6 @@
 #include <memory>
 #include <mutex>
 
-#define XTALOPT_VER_MAJOR 13
-#define XTALOPT_VER_MINOR 0
-
 // Forward declarations...
 struct latticeStruct;