Merge branch 'publicGithubDevelop' into release1.0

Conflicts:
	Doxyfile
	doc/manual/manual.tex
	utils/dftParameters.cc

Author: dsambit

.github/workflows/documentation.yml

@@ -0,0 +1,35 @@
+name: documentation
+
+# Controls when the action will run. Triggers the workflow on push or pull request
+# events but only for the master branch
+on:
+  push:
+    branches: [ publicGithubDevelop ]
+
+jobs:
+  build-documentation:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: config
+      run: |
+        git config --global init.defaultBranch publicGithubDevelop  
+  
+    # Build the HTML documentation
+    - name: Doxygen Action
+      uses: mattnotmitt/doxygen-action@v1.1.0
+      with:
+          doxyfile-path: ./Doxyfile
+          working-directory: .
+    
+    # Deploy the HTML documentation to GitHub Pages
+    - name: GH Pages Deployment
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./doc/html/
+        enable_jekyll: false
+        allow_empty_commit: false
+        force_orphan: true
+        publish_branch: gh-pages

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = "DFT-FE"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "1.0.0"
+PROJECT_NUMBER         = "1.0.1"
 
 # 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
@@ -58,7 +58,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = docs
+OUTPUT_DIRECTORY       = ./doc/
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and

doc/manual/manual.tex

@@ -136,7 +136,7 @@
 \hfill{\Huge \fontfamily{\sfdefault}\selectfont User Manual \\
 \raggedleft \huge \fontfamily{\sfdefault}\selectfont Version
 % keep the following line as is so that we can replace this using a script:
-1.0.0 %VERSION-INFO%
+1.0.1 %VERSION-INFO%
 \\\large(generated \today)\\
 \vspace{1.5em}
 {\Large Sambit Das\,\\Vikram Gavini\,\\Phani Motamarri\\}

src/dft/densityCalculatorCUDA.cu

@@ -298,6 +298,22 @@ namespace dftfe
           isEvaluateGradRho ? (cellsBlockSize * numQuadPoints * BVec) : 1,
           zero);
 
+      cudaUtils::Vector<NumberType, dftfe::MemorySpace::Host> rhoHost;
+      cudaUtils::Vector<NumberType, dftfe::MemorySpace::Host> gradRhoHostX;
+      cudaUtils::Vector<NumberType, dftfe::MemorySpace::Host> gradRhoHostY;
+      cudaUtils::Vector<NumberType, dftfe::MemorySpace::Host> gradRhoHostZ;
+
+      rhoHost.resize(totalLocallyOwnedCells * numQuadPoints, zero);
+
+      if (isEvaluateGradRho)
+        {
+          gradRhoHostX.resize(totalLocallyOwnedCells * numQuadPoints, zero);
+
+          gradRhoHostY.resize(totalLocallyOwnedCells * numQuadPoints, zero);
+          gradRhoHostZ.resize(totalLocallyOwnedCells * numQuadPoints, zero);
+        }
+
+
       NumberType *shapeFunctionValuesInvertedDevice;
 
       CUDACHECK(
@@ -364,35 +380,10 @@ namespace dftfe
         reinterpret_cast<NumberType *>(thrust::raw_pointer_cast(
           &operatorMatrix.getCellWaveFunctionMatrix()[0]));
 
-      // set density to zero
       typename dealii::DoFHandler<3>::active_cell_iterator cell =
         dofHandler.begin_active();
       typename dealii::DoFHandler<3>::active_cell_iterator endc =
         dofHandler.end();
-      for (; cell != endc; ++cell)
-        if (cell->is_locally_owned())
-          {
-            const dealii::CellId cellid = cell->id();
-
-            std::fill((*rhoValues)[cellid].begin(),
-                      (*rhoValues)[cellid].end(),
-                      0.0);
-            if (isEvaluateGradRho)
-              std::fill((*gradRhoValues)[cellid].begin(),
-                        (*gradRhoValues)[cellid].end(),
-                        0.0);
-
-            if (dftParameters::spinPolarized == 1)
-              {
-                std::fill((*rhoValuesSpinPolarized)[cellid].begin(),
-                          (*rhoValuesSpinPolarized)[cellid].end(),
-                          0.0);
-                if (isEvaluateGradRho)
-                  std::fill((*gradRhoValuesSpinPolarized)[cellid].begin(),
-                            (*gradRhoValuesSpinPolarized)[cellid].end(),
-                            0.0);
-              }
-          }
 
       std::vector<double> rhoValuesFlattened(totalLocallyOwnedCells *
                                                numQuadPoints,
@@ -1063,38 +1054,23 @@ namespace dftfe
 
 
               // do cuda memcopy to host
-              cudaUtils::Vector<NumberType, dftfe::MemorySpace::Host> rhoHost;
-              cudaUtils::Vector<NumberType, dftfe::MemorySpace::Host>
-                gradRhoHostX;
-              cudaUtils::Vector<NumberType, dftfe::MemorySpace::Host>
-                gradRhoHostY;
-              cudaUtils::Vector<NumberType, dftfe::MemorySpace::Host>
-                gradRhoHostZ;
-
-              rhoHost.resize(totalLocallyOwnedCells * numQuadPoints, zero);
               cudaUtils::copyCUDAVecToHostVec(rhoDevice.begin(),
                                               rhoHost.begin(),
                                               totalLocallyOwnedCells *
                                                 numQuadPoints);
 
               if (isEvaluateGradRho)
                 {
-                  gradRhoHostX.resize(totalLocallyOwnedCells * numQuadPoints,
-                                      zero);
                   cudaUtils::copyCUDAVecToHostVec(gradRhoDeviceX.begin(),
                                                   gradRhoHostX.begin(),
                                                   totalLocallyOwnedCells *
                                                     numQuadPoints);
 
-                  gradRhoHostY.resize(totalLocallyOwnedCells * numQuadPoints,
-                                      zero);
                   cudaUtils::copyCUDAVecToHostVec(gradRhoDeviceY.begin(),
                                                   gradRhoHostY.begin(),
                                                   totalLocallyOwnedCells *
                                                     numQuadPoints);
 
-                  gradRhoHostZ.resize(totalLocallyOwnedCells * numQuadPoints,
-                                      zero);
                   cudaUtils::copyCUDAVecToHostVec(gradRhoDeviceZ.begin(),
                                                   gradRhoHostZ.begin(),
                                                   totalLocallyOwnedCells *

src/dft/dft.cc

@@ -1467,7 +1467,7 @@ namespace dftfe
       }
     else
       {
-        initNoRemesh(true, true, false, true);
+        initNoRemesh(false, true, false, true);
       }
   }
 

src/dft/initBoundaryConditions.cc

@@ -283,13 +283,15 @@ dftClass<FEOrder, FEOrderElectro>::initBoundaryConditions(
           << init_pref << std::endl;
 
   if (!meshOnlyDeformed)
+  {  
     createMasterChargeIdToImageIdMaps(d_pspCutOff,
                                       d_imageIds,
                                       d_imagePositions,
                                       d_globalChargeIdToImageIdMap);
 
-  createMasterChargeIdToImageIdMaps(d_nlPSPCutOff,
+    createMasterChargeIdToImageIdMaps(d_nlPSPCutOff,
                                     d_imageIdsTrunc,
                                     d_imagePositionsTrunc,
                                     d_globalChargeIdToImageIdMapTrunc);
+  }
 }

src/dft/psiInitialGuess.cc

@@ -402,6 +402,7 @@ dftClass<FEOrder, FEOrderElectro>::readPSIRadialValues()
 
   boost::math::normal normDist;
   bool                pp = false;
+  std::srand(this_mpi_process);
   for (unsigned int dof = 0; dof < numberDofs; dof++)
     {
       const dealii::types::global_dof_index dofID = locallyOwnedDOFs[dof];

src/geoOpt/geoOptCell.cc

@@ -198,6 +198,7 @@ namespace dftfe
       tol * 2.0; // Dummy parameter for CGPRP, the actual stopping criteria are
                  // the Wolfe conditions and maxLineSearchIter
     const double       lineSearchDampingParameter = 0.5;
+    const double       maxUpdateInAnyComponent = 0.2;
     const unsigned int maxLineSearchIter =
       dftParameters::maxLineSearchIterCGPRP;
     const unsigned int debugLevel =
@@ -212,7 +213,8 @@ namespace dftfe
                                   mpi_communicator,
                                   lineSearchTol,
                                   maxLineSearchIter,
-                                  lineSearchDampingParameter);
+                                  lineSearchDampingParameter,
+                                  maxUpdateInAnyComponent);
 
     if (dftParameters::chkType >= 1 && dftParameters::restartFromChk)
       pcout