Merge branch 'master' into pr-cc-refactoring

# Conflicts: # src/madness/chem/CMakeLists.txt
m-a-d-n-e-s-s · Aug 16, 2023 · 742ae93 · 742ae93
2 parents d2d4cd7 + a9d5a14
commit 742ae93
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diff --git a/src/apps/cis/cis.cpp b/src/apps/cis/cis.cpp
@@ -6,7 +6,7 @@
  */
 
 #include <madness/chem/TDHF.h>
-#include <madness/chem/commandlineparser.h>
+#include <madness/mra/commandlineparser.h>
 #include <madness/misc/info.h>
 #include <madness/world/worldmem.h>
 

diff --git a/src/apps/moldft/moldft.cc b/src/apps/moldft/moldft.cc
@@ -37,7 +37,7 @@
 /// \defgroup moldft The molecular density functional and Hartree-Fock code
 
 #include<madness/chem/SCF.h>
-#include<madness/chem/commandlineparser.h>
+#include"madness/mra/commandlineparser.h"
 #include<madness/chem/molopt.h>
 #include <madness/world/worldmem.h>
 #include <madness/misc/info.h>

diff --git a/src/apps/molresponse/response_parameters.h b/src/apps/molresponse/response_parameters.h
@@ -6,7 +6,7 @@
 #ifndef SRC_APPS_MOLRESPONSE_RESPONSE_PARAMETERS_H_
 #define SRC_APPS_MOLRESPONSE_RESPONSE_PARAMETERS_H_
 
-#include <madness/chem/QCCalculationParametersBase.h>
+#include "madness/mra/QCCalculationParametersBase.h"
 #include <madness/chem/molecule.h>
 #include <madness/chem/xcfunctional.h>
 #include <madness/mra/mra.h>

diff --git a/src/apps/plot/plot2cube.cpp b/src/apps/plot/plot2cube.cpp
@@ -1,6 +1,6 @@
 #include <madness/mra/mra.h>
 #include <madness/mra/funcplot.h>
-#include <madness/chem/commandlineparser.h>
+#include "madness/mra/commandlineparser.h"
 #include <madness/chem/CalculationParameters.h>
 #include <madness/chem/molecule.h>
 

diff --git a/src/apps/plot/plot2plane.cpp b/src/apps/plot/plot2plane.cpp
@@ -1,6 +1,6 @@
 #include <madness/mra/mra.h>
 #include <madness/mra/funcplot.h>
-#include <madness/chem/commandlineparser.h>
+#include "madness/mra/commandlineparser.h"
 #include <madness/chem/CalculationParameters.h>
 #include <madness/chem/molecule.h>
 

diff --git a/src/examples/density_smoothing.cc b/src/examples/density_smoothing.cc
@@ -40,7 +40,7 @@
 
  */
 #include "smooth.h"
-#include<madness/chem/commandlineparser.h>
+#include"madness/mra/commandlineparser.h"
 #include<madness/misc/info.h>
 
 

diff --git a/src/examples/helium_exact.cc b/src/examples/helium_exact.cc
@@ -51,7 +51,7 @@
 #include<madness/chem/nemo.h>
 #include<madness/chem/correlationfactor.h>
 #include<madness/chem/electronic_correlation_factor.h>
-#include<madness/chem/commandlineparser.h>
+#include"madness/mra/commandlineparser.h"
 
 
 // switch the electronic interaction on or off

diff --git a/src/madchem.h b/src/madchem.h
@@ -29,7 +29,7 @@
 #include<madness/chem/PNOParameters.h>
 #include<madness/chem/PNOStructures.h>
 #include<madness/chem/PNOTensors.h>
-#include<madness/chem/QCCalculationParametersBase.h>
+#include"madness/mra/QCCalculationParametersBase.h"
 #include<madness/chem/QCPropertyInterface.h>
 #include<madness/chem/SCF.h>
 #include<madness/chem/SCFOperators.h>
@@ -38,7 +38,7 @@
 #include<madness/chem/atomutil.h>
 #include<madness/chem/basis.h>
 #include<madness/chem/ccpairfunction.h>
-#include<madness/chem/commandlineparser.h>
+#include"madness/mra/commandlineparser.h"
 #include<madness/chem/corepotential.h>
 #include<madness/chem/correlationfactor.h>
 #include<madness/chem/diamagneticpotentialfactor.h>

diff --git a/src/madness/chem/CC2.cc b/src/madness/chem/CC2.cc
@@ -7,7 +7,7 @@
 
 
 #include<madness/chem/CC2.h>
-#include<madness/chem/commandlineparser.h>
+#include<madness/mra/commandlineparser.h>
 #include "MolecularOrbitals.h"
 #include "localizer.h"
 

diff --git a/src/madness/chem/CCStructures.h b/src/madness/chem/CCStructures.h
@@ -11,9 +11,9 @@
 #define CCSTRUCTURES_H_
 
 #include <madness/mra/mra.h>
-#include<madness/chem/commandlineparser.h>
+#include<madness/mra/commandlineparser.h>
 #include<madness/chem/ccpairfunction.h>
-#include<madness/chem/QCCalculationParametersBase.h>
+#include<madness/mra/QCCalculationParametersBase.h>
 #include <algorithm>
 #include <iomanip>
 #include <iostream>

diff --git a/src/madness/chem/CMakeLists.txt b/src/madness/chem/CMakeLists.txt
@@ -13,7 +13,6 @@ set(MADCHEM_HEADERS
     ccpairfunction.h
     CCPotentials.h
     CCStructures.h
-    commandlineparser.h
     corepotential.h
     correlationfactor.h
     diamagneticpotentialfactor.h
@@ -49,7 +48,6 @@ set(MADCHEM_HEADERS
     polynomial.h
     potentialmanager.h
     projector.h
-    QCCalculationParametersBase.h
     QCPropertyInterface.h
     SCF.h
     SCFOperators.h
@@ -88,7 +86,6 @@ set(MADCHEM_SOURCES
     pcm.cc
     pointgroupsymmetry.cc
     polynomial.cc
-    QCCalculationParametersBase.cc
     SCF.cc
     SCFOperators.cc
     TDHF.cc
@@ -143,7 +140,7 @@ if(BUILD_TESTING)
   SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
   # The list of unit test source files
   set(CHEM_TEST_SOURCES_SHORT test_pointgroupsymmetry.cc test_masks_and_boxes.cc
-  test_QCCalculationParametersBase.cc test_qc.cc test_MolecularOrbitals.cc test_BSHApply.cc)
+  test_qc.cc test_MolecularOrbitals.cc test_BSHApply.cc)
   set(CHEM_TEST_SOURCES_LONG test_localizer.cc test_ccpairfunction.cc test_low_rank_function.cc)
   if (LIBXC_FOUND)
     list(APPEND CHEM_TEST_SOURCES_SHORT test_dft.cc )

diff --git a/src/madness/chem/CalculationParameters.h b/src/madness/chem/CalculationParameters.h
@@ -42,8 +42,8 @@
 
 #include<madness/chem/molecule.h>
 #include<madness/chem/molecularbasis.h>
-#include<madness/chem/QCCalculationParametersBase.h>
-#include<madness/chem/commandlineparser.h>
+#include<madness/mra/QCCalculationParametersBase.h>
+#include<madness/mra/commandlineparser.h>
 
 
 namespace madness {

diff --git a/src/madness/chem/SCF.h b/src/madness/chem/SCF.h
@@ -46,7 +46,7 @@
 #include <madness/mra/mra.h>
 
 #include<madness/chem/CalculationParameters.h>
-#include<madness/chem/commandlineparser.h>
+#include"madness/mra/commandlineparser.h"
 #include<madness/chem/molecule.h>
 #include<madness/chem/molecularbasis.h>
 #include<madness/chem/corepotential.h>

diff --git a/src/madness/chem/TDHF.cc b/src/madness/chem/TDHF.cc
@@ -10,7 +10,7 @@
 #include<madness/chem/oep.h>
 #include<madness/world/test_utilities.h>
 #include<madness/chem/write_test_input.h>
-#include<madness/chem/commandlineparser.h>
+#include"madness/mra/commandlineparser.h"
 
 
 namespace madness {

diff --git a/src/madness/chem/TDHF.h b/src/madness/chem/TDHF.h
@@ -15,7 +15,7 @@
 #include<madness/chem/SCFOperators.h>
 #include <math.h>
 #include<madness/chem/GuessFactory.h>
-#include<madness/chem/commandlineparser.h>
+#include"madness/mra/commandlineparser.h"
 
 
 namespace madness {

diff --git a/src/madness/chem/ccpairfunction.h b/src/madness/chem/ccpairfunction.h
@@ -8,8 +8,8 @@
 
 
 #include <madness/mra/mra.h>
-#include<madness/chem/commandlineparser.h>
-#include<madness/chem/QCCalculationParametersBase.h>
+#include<madness/mra/commandlineparser.h>
+#include<madness/mra/QCCalculationParametersBase.h>
 #include <algorithm>
 #include <iomanip>
 #include <madness/mra/macrotaskq.h>

diff --git a/src/madness/chem/molecular_optimizer.h b/src/madness/chem/molecular_optimizer.h
@@ -38,7 +38,7 @@
 
 #include <madness/tensor/solvers.h>
 #include<madness/chem/molecule.h>
-#include<madness/chem/QCCalculationParametersBase.h>
+#include"madness/mra/QCCalculationParametersBase.h"
 
 namespace madness {
 

diff --git a/src/madness/chem/molecule.cc b/src/madness/chem/molecule.cc
@@ -459,7 +459,7 @@ nlohmann::json Molecule::to_json() const {
     mol_schema["symbols"] = {};
     mol_schema["geometry"] = {};
 
-    get_atomic_data(atoms[0].atomic_number).symbol;
+//    get_atomic_data(atoms[0].atomic_number).symbol;
     for (size_t i = 0; i < natom(); ++i) {
         mol_schema["symbols"].push_back(get_atomic_data(atoms[i].atomic_number).symbol);
         mol_schema["geometry"].push_back({atoms[i].x, atoms[i].y, atoms[i].z});

diff --git a/src/madness/chem/molecule.h b/src/madness/chem/molecule.h
@@ -37,8 +37,8 @@
 
 #include<madness/chem/corepotential.h>
 #include<madness/chem/atomutil.h>
-#include<madness/chem/commandlineparser.h>
-#include<madness/chem/QCCalculationParametersBase.h>
+#include"madness/mra/commandlineparser.h"
+#include"madness/mra/QCCalculationParametersBase.h"
 #include <madness/world/vector.h>
 #include <vector>
 #include <string>

diff --git a/src/madness/chem/mp2.h b/src/madness/chem/mp2.h
@@ -41,7 +41,7 @@
 
 #include <madness/mra/mra.h>
 #include <madness/mra/lbdeux.h>
-#include<madness/chem/QCCalculationParametersBase.h>
+#include"madness/mra/QCCalculationParametersBase.h"
 #include<madness/chem/SCF.h>
 #include <madness/mra/nonlinsol.h>
 #include<madness/chem/projector.h>

diff --git a/src/madness/chem/nemo.h b/src/madness/chem/nemo.h
@@ -56,7 +56,7 @@
 #include<madness/chem/pcm.h>
 #include<madness/chem/AC.h>
 #include<madness/chem/pointgroupsymmetry.h>
-#include<madness/chem/commandlineparser.h>
+#include"madness/mra/commandlineparser.h"
 #include<madness/chem/QCPropertyInterface.h>
 #include <madness/world/timing_utilities.h>
 

diff --git a/src/madness/chem/znemo.h b/src/madness/chem/znemo.h
@@ -10,7 +10,7 @@
 
 #include <madness/chem/CalculationParameters.h>
 #include <madness/chem/MolecularOrbitals.h>
-#include <madness/chem/QCCalculationParametersBase.h>
+#include "madness/mra/QCCalculationParametersBase.h"
 #include <madness/chem/SCFOperators.h>
 #include <madness/chem/molecular_optimizer.h>
 #include <madness/chem/molecularbasis.h>

diff --git a/src/madness/mra/CMakeLists.txt b/src/madness/mra/CMakeLists.txt
@@ -9,10 +9,11 @@ set(MADMRA_HEADERS
     mraimpl.h  funcplot.h  function_common_data.h function_factory.h
     function_interface.h gfit.h convolution1d.h simplecache.h derivative.h
     displacements.h functypedefs.h sdf_shape_3D.h sdf_domainmask.h vmra1.h
-    leafop.h nonlinsol.h macrotaskq.h macrotaskpartitioner.h)
+    leafop.h nonlinsol.h macrotaskq.h macrotaskpartitioner.h QCCalculationParametersBase.h
+    commandlineparser.h)
 set(MADMRA_SOURCES
     mra1.cc mra2.cc mra3.cc mra4.cc mra5.cc mra6.cc startup.cc legendre.cc 
-    twoscale.cc qmprop.cc)
+    twoscale.cc qmprop.cc QCCalculationParametersBase.cc)
 
 # Create the MADmra library
 add_mad_library(mra MADMRA_SOURCES MADMRA_HEADERS "linalg;tinyxml;muparser" "madness/mra")
@@ -36,7 +37,7 @@ if(BUILD_TESTING)
   set(MRA_TEST_SOURCES testbsh.cc testproj.cc 
       testpdiff.cc testdiff1Db.cc testgconv.cc testopdir.cc testinnerext.cc 
       testgaxpyext.cc testvmra.cc, test_vectormacrotask.cc test_cloud.cc
-      test_macrotaskpartitioner.cc)
+      test_macrotaskpartitioner.cc test_QCCalculationParametersBase.cc)
   add_unittests(mra "${MRA_TEST_SOURCES}" "MADmra;MADgtest" "unittests;short")
   set(MRA_SEPOP_TEST_SOURCES testsuite.cc
       testper.cc)

diff --git a/...dness/chem/QCCalculationParametersBase.cc → ...adness/mra/QCCalculationParametersBase.cc b/...dness/chem/QCCalculationParametersBase.cc → ...adness/mra/QCCalculationParametersBase.cc
@@ -5,11 +5,11 @@
  *      Author: fbischoff
  */
 
-#include<madness/chem/QCCalculationParametersBase.h>
+#include"QCCalculationParametersBase.h"
 #include <iostream>
 #include <fstream>
 #include <iomanip>
-#include<madness/world/worldgop.h>
+#include"worldgop.h"
 
 
 

diff --git a/...adness/chem/QCCalculationParametersBase.h → ...madness/mra/QCCalculationParametersBase.h b/...adness/chem/QCCalculationParametersBase.h → ...madness/mra/QCCalculationParametersBase.h
@@ -15,11 +15,11 @@
 #include <map>
 #include <fstream>
 #include <typeinfo>
-#include <madness/misc/misc.h>
-#include <madness/world/archive.h>
-#include <madness/world/world.h>
-#include<madness/chem/commandlineparser.h>
-#include<madness/external/nlohmann_json/json.hpp>
+#include "madness/misc/misc.h"
+#include "archive.h"
+#include "world.h"
+#include"commandlineparser.h"
+#include"madness/external/nlohmann_json/json.hpp"
 
 
 namespace madness {

diff --git a/src/madness/chem/commandlineparser.h → src/madness/mra/commandlineparser.h b/src/madness/chem/commandlineparser.h → src/madness/mra/commandlineparser.h