Added ion relaxation ctest. ctests passed

src/dft/moveAtoms.cc

@@ -165,9 +165,13 @@ void dftClass<FEOrder>::updateAtomPositionsAndMoveMesh(const std::vector<Point<C
 
  if (!useHybridMeshUpdateScheme)//always remesh
  {
- pcout << "Auto remeshing and reinitialization of dft problem for new atom coordinates" << std::endl;
+ if (!dftParameters::reproducible_output)
+ pcout << "Auto remeshing and reinitialization of dft problem for new atom coordinates" << std::endl;
+
  init(1);
- pcout << "...Reinitialization end" << std::endl;
+
+ if (!dftParameters::reproducible_output)
+ pcout << "...Reinitialization end" << std::endl;
  }
  else
  {

src/geoOpt/geoOptIon.cc

@@ -35,7 +35,7 @@ geoOptIon<FEOrder>::geoOptIon(dftClass<FEOrder>* _dftPtr,const MPI_Comm &mpi_com
  mpi_communicator (mpi_comm_replica),
  n_mpi_processes (Utilities::MPI::n_mpi_processes(mpi_comm_replica)),
  this_mpi_process (Utilities::MPI::this_mpi_process(mpi_comm_replica)),
- pcout(std::cout, (Utilities::MPI::this_mpi_process(MPI_COMM_WORLD) == 0))
+ pcout(std::cout, (Utilities::MPI::this_mpi_process(MPI_COMM_WORLD) == 0 && !dftParameters::reproducible_output))
 {
 
 }
@@ -84,9 +84,9 @@ void geoOptIon<FEOrder>::run()
  lineSearchDampingParameter);
 
  if (dftParameters::chkType>=1 && dftParameters::restartFromChk)
- pcout<<" Re starting Ion force relaxation using nonlinear CG solver... "<<std::endl;
+ pcout<<"Re starting Ion force relaxation using nonlinear CG solver... "<<std::endl;
  else
- pcout<<" Starting Ion force relaxation using nonlinear CG solver... "<<std::endl;
+ pcout<<"Starting Ion force relaxation using nonlinear CG solver... "<<std::endl;
  if (dftParameters::verbosity>=2)
  {
  pcout<<" ---Non-linear CG Parameters-------------- "<<std::endl;

tests/dft/pseudopotential/real/nitrogenMolecule_01.mpirun=10.output

@@ -0,0 +1,68 @@
+number of atoms: 2
+number of atoms types: 1
+-----------Simulation Domain bounding vectors (lattice vectors in fully periodic case)-------------
+v1 : 8.000000000000000000e+01 0.000000000000000000e+00 0.000000000000000000e+00
+v2 : 0.000000000000000000e+00 8.000000000000000000e+01 0.000000000000000000e+00
+v3 : 0.000000000000000000e+00 0.000000000000000000e+00 8.000000000000000000e+01
+-----------------------------------------------------------------------------------------
+------------Cartesian coordinates of atoms (origin at center of domain)------------------
+AtomId 0: -1.199999999999999956e+00 0.000000000000000000e+00 0.000000000000000000e+00
+AtomId 1: 1.199999999999999956e+00 0.000000000000000000e+00 0.000000000000000000e+00
+-----------------------------------------------------------------------------------------
+
+Finite element mesh information
+-------------------------------------------------
+number of elements: 960
+number of degrees of freedom: 31257
+-------------------------------------------------
+
+Setting initial guess for wavefunctions....
+
+Reading initial guess for electron-density.....
+
+Pseudopotential initalization....
+
+Starting SCF iterations....
+SCF iterations converged to the specified tolerance after: 12 iterations.
+
+Energy computations (Hartree) 
+-------------------
+ Total energy: -19.83481668
+
+Absolute values of ion forces (Hartree/Bohr)
+--------------------------------------------------------------------------------------------
+AtomId 0: 0.243134,0.000000,0.000000
+AtomId 1: 0.243131,0.000000,0.000000
+--------------------------------------------------------------------------------------------
+-----------Simulation Domain bounding vectors (lattice vectors in fully periodic case)-------------
+v1 : 80.000000 0.000000 0.000000
+v2 : 0.000000 80.000000 0.000000
+v3 : 0.000000 0.000000 80.000000
+-----------------------------------------------------------------------------------------
+------------Cartesian coordinates of atoms (origin at center of domain)------------------
+AtomId 0: -1.029807 0.000000 0.000000
+AtomId 1: 1.029808 0.000000 0.000000
+-----------------------------------------------------------------------------------------
+
+Finite element mesh information
+-------------------------------------------------
+number of elements: 960
+number of degrees of freedom: 31257
+-------------------------------------------------
+
+Reading initial guess for PSI....
+
+Pseudopotential initalization....
+
+Starting SCF iterations....
+SCF iterations converged to the specified tolerance after: 13 iterations.
+
+Energy computations (Hartree) 
+-------------------
+ Total energy: -19.88861003
+
+Absolute values of ion forces (Hartree/Bohr)
+--------------------------------------------------------------------------------------------
+AtomId 0: 0.078653,0.000000,0.000000
+AtomId 1: 0.078651,0.000000,0.000000
+--------------------------------------------------------------------------------------------

tests/dft/pseudopotential/real/nitrogenMolecule_01.mpirun=13.output

@@ -0,0 +1,68 @@
+number of atoms: 2
+number of atoms types: 1
+-----------Simulation Domain bounding vectors (lattice vectors in fully periodic case)-------------
+v1 : 8.000000000000000000e+01 0.000000000000000000e+00 0.000000000000000000e+00
+v2 : 0.000000000000000000e+00 8.000000000000000000e+01 0.000000000000000000e+00
+v3 : 0.000000000000000000e+00 0.000000000000000000e+00 8.000000000000000000e+01
+-----------------------------------------------------------------------------------------
+------------Cartesian coordinates of atoms (origin at center of domain)------------------
+AtomId 0: -1.199999999999999956e+00 0.000000000000000000e+00 0.000000000000000000e+00
+AtomId 1: 1.199999999999999956e+00 0.000000000000000000e+00 0.000000000000000000e+00
+-----------------------------------------------------------------------------------------
+
+Finite element mesh information
+-------------------------------------------------
+number of elements: 960
+number of degrees of freedom: 31257
+-------------------------------------------------
+
+Setting initial guess for wavefunctions....
+
+Reading initial guess for electron-density.....
+
+Pseudopotential initalization....
+
+Starting SCF iterations....
+SCF iterations converged to the specified tolerance after: 12 iterations.
+
+Energy computations (Hartree) 
+-------------------
+ Total energy: -19.83481668
+
+Absolute values of ion forces (Hartree/Bohr)
+--------------------------------------------------------------------------------------------
+AtomId 0: 0.243134,0.000000,0.000000
+AtomId 1: 0.243131,0.000000,0.000000
+--------------------------------------------------------------------------------------------
+-----------Simulation Domain bounding vectors (lattice vectors in fully periodic case)-------------
+v1 : 80.000000 0.000000 0.000000
+v2 : 0.000000 80.000000 0.000000
+v3 : 0.000000 0.000000 80.000000
+-----------------------------------------------------------------------------------------
+------------Cartesian coordinates of atoms (origin at center of domain)------------------
+AtomId 0: -1.029806 0.000000 0.000000
+AtomId 1: 1.029808 0.000000 0.000000
+-----------------------------------------------------------------------------------------
+
+Finite element mesh information
+-------------------------------------------------
+number of elements: 960
+number of degrees of freedom: 31257
+-------------------------------------------------
+
+Reading initial guess for PSI....
+
+Pseudopotential initalization....
+
+Starting SCF iterations....
+SCF iterations converged to the specified tolerance after: 12 iterations.
+
+Energy computations (Hartree) 
+-------------------
+ Total energy: -19.88861002
+
+Absolute values of ion forces (Hartree/Bohr)
+--------------------------------------------------------------------------------------------
+AtomId 0: 0.078646,0.000000,0.000000
+AtomId 1: 0.078646,0.000000,0.000000
+--------------------------------------------------------------------------------------------

tests/dft/pseudopotential/real/nitrogenMolecule_01.prm.in

@@ -0,0 +1,52 @@
+set VERBOSITY = 0
+set REPRODUCIBLE OUTPUT = true
+
+subsection Geometry
+ set NATOMS=2
+ set NATOM TYPES=1
+ set ATOMIC COORDINATES FILE = @SOURCE_DIR@/nitrogenMolecule_coordinates.inp
+ set DOMAIN VECTORS FILE = @SOURCE_DIR@/nitrogenMolecule_domainVectors.inp
+ subsection Optimization
+ set ION OPT=true
+ set FORCE TOL=0.1
+ set ION RELAX FLAGS FILE =@SOURCE_DIR@/nitrogenMolecule_relaxationFlags.inp
+ end
+end
+
+subsection Boundary conditions
+ set PERIODIC1 = false
+ set PERIODIC2 = false
+ set PERIODIC3 = false
+ set SELF POTENTIAL RADIUS = 4.0
+end
+
+subsection Finite element mesh parameters
+ set POLYNOMIAL ORDER=3
+ subsection Auto mesh generation parameters
+ set MESH SIZE AROUND ATOM = 0.7
+ set BASE MESH SIZE = 10.0
+ set ATOM BALL RADIUS = 2.0
+ set MESH SIZE AT ATOM = 0.7
+ end
+end
+
+subsection DFT functional parameters
+ set EXCHANGE CORRELATION TYPE = 4
+ set PSEUDOPOTENTIAL CALCULATION = true
+ set PSEUDO TESTS FLAG = true
+ set PSEUDOPOTENTIAL FILE NAMES LIST = @SOURCE_DIR@/pseudoNGGA.inp
+end
+
+subsection SCF parameters
+ set ANDERSON SCHEME MIXING HISTORY = 70
+ set ANDERSON SCHEME MIXING PARAMETER = 0.5
+ set MAXIMUM ITERATIONS = 40
+ set TEMPERATURE = 500
+ set TOLERANCE = 5e-6
+
+ subsection Eigen-solver parameters
+ set NUMBER OF KOHN-SHAM WAVEFUNCTIONS = 12
+ set ORTHOGONALIZATION TYPE=LW
+ set CHEBYSHEV POLYNOMIAL DEGREE = 25
+ end
+end

tests/dft/pseudopotential/real/nitrogenMolecule_coordinates.inp

@@ -0,0 +1,2 @@
+7 5 -1.20000000E+00 0.00000000E+00 0.00000000E+00
+7 5 1.20000000E+00 0.00000000E+00 0.00000000E+00

tests/dft/pseudopotential/real/nitrogenMolecule_domainVectors.inp

@@ -0,0 +1,3 @@
+80.0 0.0 0.0
+0.0 80.0 0.0
+0.0 0.0 80.0

tests/dft/pseudopotential/real/nitrogenMolecule_relaxationFlags.inp

@@ -0,0 +1,2 @@
+1 0 0
+1 0 0

tests/dft/pseudopotential/real/pseudoNGGA.inp

@@ -0,0 +1 @@
+7 N_ONCV_PBE-1.0.upf