The examples were broken by the last update. I fixed them, and added …

…reference output to premade matrix
william-dawson · Aug 1, 2017 · d18d3b9 · d18d3b9
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diff --git a/Examples/GraphTheory/main.f90 b/Examples/GraphTheory/main.f90
@@ -3,12 +3,13 @@
 PROGRAM GraphTheory
   USE DataTypesModule, ONLY : ntreal
   USE DistributedSparseMatrixModule, ONLY : &
-       & WriteToMatrixMarket, DistributedSparseMatrix, ConstructEmpty, &
+       & WriteToMatrixMarket, DistributedSparseMatrix_t, &
+       & ConstructEmptyDistributedSparseMatrix, &
        & FillFromTripletList, DestructDistributedSparseMatrix, &
        & CopyDistributedSparseMatrix, FillDistributedIdentity, &
        & IncrementDistributedSparseMatrix
   USE InverseSolversModule, ONLY : Invert
-  USE IterativeSolversModule, ONLY : IterativeSolverParameters
+  USE IterativeSolversModule, ONLY : IterativeSolverParameters_t
   USE ProcessGridModule, ONLY : ConstructProcessGrid
   USE TripletListModule, ONLY : TripletList_t, ConstructTripletList, &
        & SetTripletAt, AppendToTripletList
@@ -22,15 +23,15 @@ PROGRAM GraphTheory
   CHARACTER(len=80) :: output_file
   REAL(ntreal) :: threshold
   REAL(ntreal) :: attenuation
-  TYPE(IterativeSolverParameters) :: solver_parameters
+  TYPE(IterativeSolverParameters_t) :: solver_parameters
   !! MPI Variables
   INTEGER :: rank
   INTEGER :: total_processors
   INTEGER :: ierr
   INTEGER :: provided
   !! Matrices
-  TYPE(DistributedSparseMatrix) :: NetworkMat
-  TYPE(DistributedSparseMatrix) :: ResultMat
+  TYPE(DistributedSparseMatrix_t) :: NetworkMat
+  TYPE(DistributedSparseMatrix_t) :: ResultMat
   !! Local Part of the Matrix
   INTEGER :: number_of_local_nodes
   INTEGER, DIMENSION(:), ALLOCATABLE :: local_nodes
@@ -75,14 +76,14 @@ PROGRAM GraphTheory
        & process_slices)
 
   !! Set Up The Solver Parameters.
-  solver_parameters = IterativeSolverParameters( &
+  solver_parameters = IterativeSolverParameters_t( &
        & be_verbose_in = .TRUE., threshold_in = threshold)
 
   CALL DivideUpWork
 
   !! Fill The Matrix
-  CALL ConstructEmpty(NetworkMat, number_of_nodes)
-  CALL ConstructEmpty(ResultMat, number_of_nodes)
+  CALL ConstructEmptyDistributedSparseMatrix(NetworkMat, number_of_nodes)
+  CALL ConstructEmptyDistributedSparseMatrix(ResultMat, number_of_nodes)
   CALL FillMatrix
 
   !! Solve
@@ -196,10 +197,10 @@ SUBROUTINE FillMatrix
   END SUBROUTINE FillMatrix
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   SUBROUTINE SolveMatrix
-    TYPE(DistributedSparseMatrix) :: ResMat
+    TYPE(DistributedSparseMatrix_t) :: ResMat
 
     !! Compute attenuation*Identity - Matrix
-    CALL ConstructEmpty(ResMat, number_of_nodes)
+    CALL ConstructEmptyDistributedSparseMatrix(ResMat, number_of_nodes)
     CALL FillDistributedIdentity(ResMat)
     CALL IncrementDistributedSparseMatrix(NetworkMat, ResMat, &
          & alpha_in=REAL(-1.0*attenuation,NTREAL))

diff --git a/Examples/HydrogenAtom/ReadMe.md b/Examples/HydrogenAtom/ReadMe.md
@@ -16,7 +16,7 @@ There are three main points to this example.
 
 In a somewhat unconventional manner, we will do all this using the real space
 basis set. Of course, it is normally neither practical nor useful to compute
-the density matrix in real space, however the equations in real space are
+the full density matrix in real space, however the equations in real space are
 very simple and will allow us to demonstrate the concepts.
 
 We need to solve the following equation:

diff --git a/Examples/HydrogenAtom/main.f90 b/Examples/HydrogenAtom/main.f90
@@ -4,10 +4,11 @@ PROGRAM HydrogenAtom
   USE DataTypesModule, ONLY : ntreal
   USE DensityMatrixSolversModule, ONLY : TRS2
   USE DistributedSparseMatrixModule, ONLY : &
-       & WriteToMatrixMarket, DistributedSparseMatrix, ConstructEmpty, &
+       & WriteToMatrixMarket, DistributedSparseMatrix_t, &
+       & ConstructEmptyDistributedSparseMatrix, &
        & FillFromTripletList, CopyDistributedSparseMatrix, &
        & IncrementDistributedSparseMatrix, FillDistributedIdentity
-  USE IterativeSolversModule, ONLY : IterativeSolverParameters
+  USE IterativeSolversModule, ONLY : IterativeSolverParameters_t
   USE PermutationModule, ONLY : Permutation_t, ConstructRandomPermutation
   USE ProcessGridModule, ONLY : ConstructProcessGrid
   USE SquareRootSolversModule, ONLY : InverseSquareRoot
@@ -21,7 +22,7 @@ PROGRAM HydrogenAtom
   CHARACTER(len=80) :: density_file_out
   INTEGER :: process_rows, process_columns, process_slices
   REAL(ntreal) :: threshold, convergence_threshold
-  TYPE(IterativeSolverParameters) :: solver_parameters
+  TYPE(IterativeSolverParameters_t) :: solver_parameters
   !! MPI Variables
   INTEGER :: rank
   INTEGER :: total_processors
@@ -36,11 +37,11 @@ PROGRAM HydrogenAtom
   REAL(ntreal) :: grid_spacing
   REAL(ntreal), DIMENSION(:), ALLOCATABLE :: x_values
   !! Matrices
-  TYPE(DistributedSparseMatrix) :: KineticEnergy
-  TYPE(DistributedSparseMatrix) :: PotentialEnergy
-  TYPE(DistributedSparseMatrix) :: Hamiltonian
-  TYPE(DistributedSparseMatrix) :: Identity
-  TYPE(DistributedSparseMatrix) :: Density
+  TYPE(DistributedSparseMatrix_t) :: KineticEnergy
+  TYPE(DistributedSparseMatrix_t) :: PotentialEnergy
+  TYPE(DistributedSparseMatrix_t) :: Hamiltonian
+  TYPE(DistributedSparseMatrix_t) :: Identity
+  TYPE(DistributedSparseMatrix_t) :: Density
   !! Temporary Variables
   CHARACTER(len=80) :: argument
   CHARACTER(len=80) :: argument_value
@@ -78,7 +79,7 @@ PROGRAM HydrogenAtom
        & process_slices)
 
   !! Set Up The Solver Parameters.
-  solver_parameters = IterativeSolverParameters( be_verbose_in=.TRUE., &
+  solver_parameters = IterativeSolverParameters_t( be_verbose_in=.TRUE., &
        & converge_diff_in=convergence_threshold, threshold_in=threshold)
 
   !! Divide The Work Amongst Processors.
@@ -88,19 +89,20 @@ PROGRAM HydrogenAtom
   CALL ConstructLinearSpace()
 
   !! Construct The Kinetic Energy Operator.
-  CALL ConstructEmpty(KineticEnergy, grid_points)
+  CALL ConstructEmptyDistributedSparseMatrix(KineticEnergy, grid_points)
   CALL FillKineticEnergy()
 
   !! Construct The Potential Energy Operator.
-  CALL ConstructEmpty(PotentialEnergy, grid_points)
+  CALL ConstructEmptyDistributedSparseMatrix(PotentialEnergy, grid_points)
   CALL FillPotentialEnergy()
 
   !! Construct The Full Hamiltonian.
   CALL CopyDistributedSparseMatrix(KineticEnergy, Hamiltonian)
   CALL IncrementDistributedSparseMatrix(PotentialEnergy, Hamiltonian)
 
   !! Overlap Matrix is just the identity.
-  CALL ConstructEmpty(Identity,Hamiltonian%actual_matrix_dimension)
+  CALL ConstructEmptyDistributedSparseMatrix(Identity, &
+       & Hamiltonian%actual_matrix_dimension)
   CALL FillDistributedIdentity(Identity)
 
   !! Call the solver routine.

diff --git a/Examples/HydrogenAtom/main.py b/Examples/HydrogenAtom/main.py
@@ -117,8 +117,8 @@
     # Call the solver routine.
     chemical_potential = 0
     Density = nt.DistributedSparseMatrix(grid_points)
-    nt.DensityMatrixSolvers.TRS2(Hamiltonian, Identity, 2,
-                                 Density, chemical_potential, solver_parameters)
+    chemical_potential = nt.DensityMatrixSolvers.TRS2(Hamiltonian, Identity, 2,
+                                 Density, solver_parameters)
 
     # Print the density matrix to file.
     Density.WriteToMatrixMarket(density_file_out)
diff --git a/Examples/HydrogenAtom/visualize.py b/Examples/HydrogenAtom/visualize.py
@@ -2,7 +2,7 @@
 import matplotlib.pyplot as plt
 import numpy
 
-# A function that reads in matrix market-esque files produced by the library.
+# A function that reads in matrix market files produced by the library.
 # @param file_name file to read.
 def ReadMM(file_name):
     matrix = numpy.zeros((0, 0))

diff --git a/Examples/OverlapMatrix/main.f90 b/Examples/OverlapMatrix/main.f90
@@ -14,10 +14,10 @@ PROGRAM OverlapExample
   !! Parameters
   INTEGER :: process_rows, process_columns, process_slices
   REAL(ntreal) :: threshold, convergence_threshold
-  TYPE(IterativeSolverParameters) :: solver_parameters
+  TYPE(IterativeSolverParameters_t) :: solver_parameters
   INTEGER :: basis_functions
   !! Matrices
-  TYPE(DistributedSparseMatrix) :: Overlap, ISQOverlap
+  TYPE(DistributedSparseMatrix_t) :: Overlap, ISQOverlap
   TYPE(Permutation_t) :: permutation
   !! Triplet List
   TYPE(TripletList_t) :: triplet_list
@@ -79,8 +79,8 @@ PROGRAM OverlapExample
   end_column = start_column + local_columns - 1
 
   !! Build The Empty Matrices
-  CALL ConstructEmpty(Overlap, basis_functions)
-  CALL ConstructEmpty(ISQOverlap, basis_functions)
+  CALL ConstructEmptyDistributedSparseMatrix(Overlap, basis_functions)
+  CALL ConstructEmptyDistributedSparseMatrix(ISQOverlap, basis_functions)
 
   !! Compute The Overlap Matrix
   CALL StartTimer("Construct Triplet List")
@@ -105,7 +105,7 @@ PROGRAM OverlapExample
   !! Set Up The Solver Parameters.
   CALL ConstructRandomPermutation(permutation, &
        & Overlap%logical_matrix_dimension)
-  solver_parameters = IterativeSolverParameters(&
+  solver_parameters = IterativeSolverParameters_t(&
        & converge_diff_in=convergence_threshold, threshold_in=threshold, &
        & BalancePermutation_in=permutation, be_verbose_in=.TRUE.)
 

diff --git a/Examples/OverlapMatrix/visualize.py b/Examples/OverlapMatrix/visualize.py
@@ -3,7 +3,7 @@
 import numpy
 from matplotlib.colors import LogNorm
 
-# A function that reads in matrix market-esque files produced by the library.
+# A function that reads in matrix market files produced by the library.
 # @param file_name file to read.
 def ReadMM(file_name):
     matrix = numpy.zeros((0, 0))

diff --git a/Examples/PremadeMatrix/Density-Reference.mtx b/Examples/PremadeMatrix/Density-Reference.mtx
@@ -0,0 +1,40 @@
+%%MatrixMarket matrix coordinate real general
+%
+            7           7                   37
+            1           1   1.0549095967421220      
+            2           1 -0.23302213379033082      
+            3           1   3.7646419335116699E-002 
+            4           1   3.7646419335116685E-002 
+            6           1  -7.5642046773935134E-003 
+            7           1  -7.5642046773937563E-003 
+            1           2 -0.23302213783309644      
+            2           2   1.0292641102917328      
+            3           2 -0.20982918266288592      
+            4           2 -0.20982918266288578      
+            6           2  -4.3117326895678362E-002 
+            7           2  -4.3117326895676926E-002 
+            1           3   3.7646421361998791E-002 
+            2           3 -0.20982921225444917      
+            3           3  0.46883722812203843      
+            4           3   6.8501651086330564E-002 
+            6           3  0.37466965007376707      
+            7           3  -3.1414239305686278E-002 
+            1           4   3.7646421361998764E-002 
+            2           4 -0.20982921225444895      
+            3           4   6.8501651086330509E-002 
+            4           4  0.46883722812204076      
+            6           4  -3.1414239305686306E-002 
+            7           4  0.37466965007376629      
+            5           5   1.0000000000000000      
+            1           6  -7.5642029235768070E-003 
+            2           6  -4.3117329307985383E-002 
+            3           6  0.37466966035658766      
+            4           6  -3.1414332242094133E-002 
+            6           6  0.32525138744266346      
+            7           6  -8.6663457475723252E-002 
+            1           7  -7.5642029235770195E-003 
+            2           7  -4.3117329307984009E-002 
+            3           7  -3.1414332242094126E-002 
+            4           7  0.37466966035658689      
+            6           7  -8.6663457475723182E-002 
+            7           7  0.32525138744266113      
diff --git a/Examples/PremadeMatrix/ReadMe.md b/Examples/PremadeMatrix/ReadMe.md
@@ -106,3 +106,6 @@ computed by these routines.
 It is possible to write out a matrix either to either a text or binary format.
 Writing to text is slower, but is portable across systems. Writing to binary
 should probably only be used to store intermediate results.
+
+The output file can be compared to Density-Reference.mtx to verify its
+correctness. 
diff --git a/Examples/PremadeMatrix/main.f90 b/Examples/PremadeMatrix/main.f90
@@ -4,8 +4,8 @@ PROGRAM PremadeMatrixProgram
   USE DataTypesModule, ONLY : ntreal
   USE DensityMatrixSolversModule, ONLY : TRS2
   USE DistributedSparseMatrixModule, ONLY : ConstructFromMatrixMarket, &
-       & WriteToMatrixMarket, DistributedSparseMatrix
-  USE IterativeSolversModule, ONLY : IterativeSolverParameters
+       & WriteToMatrixMarket, DistributedSparseMatrix_t
+  USE IterativeSolversModule, ONLY : IterativeSolverParameters_t
   USE LoggingModule
   USE PermutationModule, ONLY : Permutation_t, ConstructRandomPermutation
   USE ProcessGridModule, ONLY : ConstructProcessGrid, IsRoot
@@ -19,12 +19,12 @@ PROGRAM PremadeMatrixProgram
   INTEGER :: process_rows, process_columns, process_slices
   REAL(ntreal) :: threshold, convergence_threshold
   INTEGER :: number_of_electrons
-  TYPE(IterativeSolverParameters) :: solver_parameters
+  TYPE(IterativeSolverParameters_t) :: solver_parameters
   TYPE(Permutation_t) :: permutation
   !! Matrices
-  TYPE(DistributedSparseMatrix) :: Hamiltonian, Overlap
-  TYPE(DistributedSparseMatrix) :: ISQOverlap
-  TYPE(DistributedSparseMatrix) :: Density
+  TYPE(DistributedSparseMatrix_t) :: Hamiltonian, Overlap
+  TYPE(DistributedSparseMatrix_t) :: ISQOverlap
+  TYPE(DistributedSparseMatrix_t) :: Density
   !! Temporary Variables
   CHARACTER(len=80) :: argument
   CHARACTER(len=80) :: argument_value
@@ -88,7 +88,7 @@ PROGRAM PremadeMatrixProgram
   !! Set Up The Solver Parameters.
   CALL ConstructRandomPermutation(permutation, &
        & Hamiltonian%logical_matrix_dimension)
-  solver_parameters = IterativeSolverParameters(&
+  solver_parameters = IterativeSolverParameters_t(&
        & converge_diff_in=convergence_threshold, threshold_in=threshold, &
        & BalancePermutation_in=permutation, be_verbose_in=.TRUE.)
 

diff --git a/Examples/PremadeMatrix/main.py b/Examples/PremadeMatrix/main.py
@@ -56,8 +56,9 @@
     # Call the solver routines.
     nt.SquareRootSolvers.InverseSquareRoot(
         Overlap, ISQOverlap, solver_parameters)
-    nt.DensityMatrixSolvers.TRS2(Hamiltonian, ISQOverlap, number_of_electrons,
-                                 Density, chemical_potential, solver_parameters)
+    chemical_potential = nt.DensityMatrixSolvers.TRS2(Hamiltonian, ISQOverlap,
+                                 number_of_electrons,
+                                 Density, solver_parameters)
 
     # Print the density matrix to file.
     Density.WriteToMatrixMarket(density_file_out)
diff --git a/ReadMe.md b/ReadMe.md
@@ -69,7 +69,8 @@ Getting Start With Examples
 --------------------------------------------------------------------------------
 In the examples directory, there are a number of different example programs that
 use NTPoly. You can check the ReadMe.md file in each example directory to
-learn how to build and run each example.
+learn how to build and run each example. The simplest example is PremadeMatrix,
+which includes sample output you can compare to.
 
 Feature Outline
 --------------------------------------------------------------------------------