Nexus: Add unit tests and example for qdens-radial tool

nexus/bin/nxs-test

@@ -1627,6 +1627,10 @@ def qdens():
 #end def qdens
 
 
+def qdens_radial():
+    nunit_all()
+#end def qdens
+
 
 def qmca():
     nunit('help')
@@ -1968,6 +1972,7 @@ NexusTest( nxs_sim                         )
 NexusTest( qmca                            )
 NexusTest( qmc_fit                         )
 NexusTest( qdens                           )
+NexusTest( qdens_radial                    )
 
 # ordered alphabetically (pytest order)
 #NexusTest( basisset                        )
@@ -2005,6 +2010,7 @@ NexusTest( qdens                           )
 #NexusTest( pyscf_input                     )
 #NexusTest( pyscf_simulation                )
 #NexusTest( qdens                           )
+#NexusTest( qdens_radial                    )
 #NexusTest( qmc_fit                         )
 #NexusTest( qmca                            )
 #NexusTest( qmcpack_analyzer                )

nexus/bin/qdens-radial

@@ -168,6 +168,10 @@ class QMCDensityRadialProcessor(QDRBase):
                           default='None',
                           help='Location of DMC+err to be used for resampling (default=%default).'
                           )
+        parser.add_option('--seed',dest='random_seed',
+                          default='None',
+                          help='Random seed used for re-sampling. (default=%default).'
+                          )
         parser.add_option('-n','--nsamples',dest='nsamples',
                           default='50',
                           help='Number of samples for resampling (default=%default).'
@@ -249,6 +253,21 @@ class QMCDensityRadialProcessor(QDRBase):
             #end if
         #end if
 
+        #   --seed option
+        if opt.random_seed is not None:
+            opt_failed = False
+            rseed = opt.random_seed
+            try:
+                opt.random_seed = int(opt.random_seed)
+            except:
+                opt_failed = True
+            #end try
+            if opt_failed:
+                self.error('seed must be an integer\nyou provided: {0}'.format(rseed))
+            #end if
+        #end if
+
+
     #end def read_command_line(self)
 
     def process(self):
@@ -337,6 +356,10 @@ class QMCDensityRadialProcessor(QDRBase):
             sum_sq_dict = {}
             std_dict = {}
 
+            if opt.random_seed is not None:
+                np.random.seed(opt.random_seed)
+            #end if
+
             nsamples = opt.nsamples
             self.log('Will compute {} samples...'.format(nsamples))
             for i in range(nsamples):

nexus/examples/qmcpack/rsqmc_misc/diamond_radial_density/diamond_spin.py

@@ -0,0 +1,122 @@
+#! /usr/bin/env python
+
+from nexus import settings
+from nexus import job
+from nexus import run_project
+from nexus import generate_physical_system
+from nexus import generate_pwscf
+from nexus import generate_projwfc
+from nexus import generate_pw2qmcpack
+from nexus import generate_qmcpack
+from nexus import vmc
+
+from structure import *
+
+from qmcpack_input import spindensity
+
+settings(
+    pseudo_dir    = '../../pseudopotentials',
+    runs          = 'runs_spin',
+    results       = '',
+    status_only   = 0,
+    generate_only = 0,
+    skip_submit   = 0,
+    sleep         = 3,
+    machine       = 'ws4'
+    )
+
+dia16 = generate_physical_system(
+    units  = 'A',
+    axes   = [[ 1.785,  1.785,  0.   ],
+              [ 0.   ,  1.785,  1.785],
+              [ 1.785,  0.   ,  1.785]],
+    elem   = ['C','C'],
+    pos    = [[ 0.    ,  0.    ,  0.    ],
+              [ 0.8925,  0.8925,  0.8925]],
+    tiling = (1,1,1),
+    C      = 4
+    )
+
+# k-mesh used for density
+scf_kg = dia16.structure.kgrid_from_kspacing(0.5) # Get SCF kmesh from k-spacing
+
+# twist-mesh used for qmc
+dia16.structure.add_symmetrized_kmesh(kgrid=(2,2,2),kshift=(0,0,0))
+
+
+number_of_ks_orbs = 11
+
+scf = generate_pwscf(
+    identifier   = 'scf',
+    path         = 'scf',
+    job          = job(cores=1,app='pw.x',hours=1),
+    input_type   = 'generic',
+    calculation  = 'scf',
+    nspin        = 2,
+    tot_magnetization = 0,
+    nbnd         = number_of_ks_orbs,
+    input_dft    = 'lda',
+    ecutwfc      = 200,
+    conv_thr     = 1e-8,
+    nosym        = False,
+    wf_collect   = False,
+    system       = dia16,
+    kgrid        = scf_kg,
+    kshift       = (0,0,0),
+    pseudos      = ['C.BFD.upf'],
+    )
+
+nscf = generate_pwscf(
+    identifier   = 'nscf',
+    path         = 'nscf',
+    job          = job(cores=1,app='pw.x',hours=1),
+    input_type   = 'generic',
+    calculation  = 'nscf',
+    input_dft    = 'lda',
+    ecutwfc      = 200,
+    nspin        = 2,
+    tot_magnetization = 0,
+    conv_thr     = 1e-8,
+    nosym        = True,
+    wf_collect   = True,
+    system       = dia16,
+    nbnd         = number_of_ks_orbs,
+    verbosity    = 'high', #verbosity must be set to high
+    pseudos      = ['C.BFD.upf'],
+    dependencies = (scf,'charge_density'),
+    )
+
+# Generate orbital h5 file
+conv = generate_pw2qmcpack(
+    identifier   = 'conv',
+    path         = 'nscf',
+    job          = job(cores=1,app='pw2qmcpack.x',hours=1),
+    write_psir   = False,
+    dependencies = (nscf,'orbitals'),
+    )
+
+
+qmc = generate_qmcpack(
+    identifier   = 'vmc',
+    path         = 'vmc',
+    job          = job(cores=3,app='qmcpack_complex',hours=1),
+    input_type   = 'basic',
+    system       = dia16,
+    pseudos      = ['C.BFD.xml'],
+    estimators   = [spindensity(dr=(0.5,0.5,0.5))],
+    jastrows     = [],
+    calculations = [
+        vmc(
+            walkers     =   1,
+            warmupsteps =  20,
+            blocks      = 200,
+            steps       =  10,
+            substeps    =   2,
+            timestep    =  .4
+            )
+        ],
+    dependencies = (conv,'orbitals'),
+    )
+
+run_project()
+

nexus/examples/qmcpack/rsqmc_misc/diamond_radial_density/qdens-radial.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+qdens-radial -s C -r 0.6 runs_spin/vmc/vmc.avg.s000.SpinDensity_u+d.xsf
+qdens-radial -s C -r 0.6 -c runs_spin/vmc/vmc.avg.s000.SpinDensity_u+d.xsf
+

nexus/examples/qmcpack/rsqmc_misc/diamond_radial_density/qdens.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+qdens -a -v -e 10 -f xsf -i runs_spin/vmc/vmc.g000.twistnum_0.in.xml runs_spin/vmc/*.stat.h5
+

nexus/tests/CMakeLists.txt

@@ -13,7 +13,7 @@ if(ADD_TEST)
   foreach(TESTNAME ${TESTLIST})
     #message("Adding test ntest_nexus_${TESTNAME}")
     set(NTEST "${qmcpack_SOURCE_DIR}/nexus/bin/nxs-test")
-    add_test(NAME ntest_nexus_${TESTNAME} COMMAND ${NTEST} -R ${TESTNAME} --ctest
+    add_test(NAME ntest_nexus_${TESTNAME} COMMAND ${NTEST} -R ${TESTNAME}\$ --ctest
                                                   --pythonpath=${PROJECT_SOURCE_DIR}/nexus/lib)
     set_property(
       TEST ntest_nexus_${TESTNAME}

nexus/tests/unit/test_qdens_radial.py

@@ -0,0 +1,157 @@
+
+import versions
+import testing
+from testing import execute,text_eq,check_value_eq
+
+
+if versions.spglib_available:
+    def test_radial_density():
+        import os
+
+        tpath = testing.setup_unit_test_output_directory('qdens_radial','test_radial_density')
+
+        exe = testing.executable_path('qdens-radial')
+
+        qr_vmc_files_path = testing.unit_test_file_path('qdens_radial','diamond_twist/vmc')
+        command = 'rsync -a {} {}'.format(qr_vmc_files_path,tpath)
+        out,err,rc = execute(command)
+        assert(rc==0)
+        vmc_path = os.path.join(tpath,'vmc')
+        vmc_infile = os.path.join(vmc_path,'vmc.g000.twistnum_0.in.xml')
+        assert(os.path.exists(vmc_infile))
+        vmc_infile = os.path.join(vmc_path,'vmc.g001.twistnum_1.in.xml')
+        assert(os.path.exists(vmc_infile))
+        vmc_infile = os.path.join(vmc_path,'vmc.g002.twistnum_2.in.xml')
+        assert(os.path.exists(vmc_infile))
+        vmc_infile = os.path.join(vmc_path,'vmc.g003.twistnum_3.in.xml')
+        assert(os.path.exists(vmc_infile))
+
+        files_bef = '''
+        vmc.avg.s000.SpinDensity_u+d+err.xsf  vmc.avg.s000.SpinDensity_u+d-err.xsf
+        vmc.avg.s000.SpinDensity_u+d.xsf      vmc.g000.twistnum_0.in.xml
+        vmc.g000.s000.scalar.dat              vmc.g001.s000.scalar.dat
+        vmc.g000.twistnum_0.in.g000.qmc       vmc.g001.twistnum_1.in.g001.qmc
+        vmc.g001.twistnum_1.in.xml            vmc.g002.twistnum_2.in.xml
+        vmc.g002.s000.scalar.dat              vmc.g003.s000.scalar.dat
+        vmc.g002.twistnum_2.in.g002.qmc       vmc.g003.twistnum_3.in.g003.qmc
+        vmc.g003.twistnum_3.in.xml            vmc.out
+        vmc.in                                vmc.info.xml
+        '''.split()
+
+        qr_dmc_files_path = testing.unit_test_file_path('qdens_radial','diamond_twist/dmc')
+        command = 'rsync -a {} {}'.format(qr_dmc_files_path,tpath)
+        out,err,rc = execute(command)
+        assert(rc==0)
+        dmc_path = os.path.join(tpath,'dmc')
+        dmc_infile = os.path.join(dmc_path,'dmc.g000.twistnum_0.in.xml')
+        assert(os.path.exists(dmc_infile))
+        dmc_infile = os.path.join(dmc_path,'dmc.g001.twistnum_1.in.xml')
+        assert(os.path.exists(dmc_infile))
+        dmc_infile = os.path.join(dmc_path,'dmc.g002.twistnum_2.in.xml')
+        assert(os.path.exists(dmc_infile))
+        dmc_infile = os.path.join(dmc_path,'dmc.g003.twistnum_3.in.xml')
+        assert(os.path.exists(dmc_infile))
+
+        files_bef = '''
+        dmc.avg.s001.SpinDensity_u+d+err.xsf  dmc.avg.s001.SpinDensity_u+d-err.xsf
+        dmc.avg.s001.SpinDensity_u+d.xsf      dmc.g001.s001.scalar.dat                               
+        dmc.g000.s000.scalar.dat              dmc.g000.s001.scalar.dat
+        dmc.g000.twistnum_0.in.g000.qmc       dmc.g001.twistnum_1.in.g001.qmc
+        dmc.g000.twistnum_0.in.xml            dmc.g001.twistnum_1.in.xml     
+        dmc.g001.s000.scalar.dat              dmc.g002.s000.scalar.dat       
+        dmc.g002.s001.scalar.dat              dmc.g003.s001.scalar.dat       
+        dmc.g002.twistnum_2.in.g002.qmc       dmc.g003.twistnum_3.in.g003.qmc
+        dmc.g002.twistnum_2.in.xml            dmc.g003.twistnum_3.in.xml
+        dmc.g003.s000.scalar.dat              dmc.in
+        dmc.out
+        '''.split()
+
+        assert(check_value_eq(set(os.listdir(dmc_path)),set(files_bef)))
+
+        # VMC non-cumulative
+        command = '{0} -s C -r 0.6 {1}/vmc.avg.s000.SpinDensity_u+d.xsf'.format(exe,vmc_path)
+        out,err,rc = execute(command)
+
+        # Assert that return code is 0
+        assert(rc==0)
+
+        # Assert that output is consistent with reference
+        out_ref = '''
+Norm:   tot             = 8.00000003
+
+Non-Cumulative Value of C Species at Cutoff 0.6 is: 4.773264912162242
+'''
+        assert(text_eq(out,out_ref))
+
+        # VMC cumulative
+        command = '{0} -s C -r 0.6 -c {1}/vmc.avg.s000.SpinDensity_u+d.xsf'.format(exe,vmc_path)
+        out,err,rc = execute(command)
+
+        # Assert that return code is 0
+        assert(rc==0)
+
+        # Assert that output is consistent with reference
+        out_ref = '''
+Norm:   tot             = 8.00000003
+
+Cumulative Value of C Species at Cutoff 0.6 is: 1.0684248641866259
+'''
+
+        # DMC extrapolated non-cumulative
+        command = '{0} -s C -r 0.6 --vmc={1}/vmc.avg.s000.SpinDensity_u+d.xsf {2}/dmc.avg.s001.SpinDensity_u+d.xsf'.format(exe,vmc_path,dmc_path)
+        out,err,rc = execute(command)
+
+        # Assert that return code is 0
+        assert(rc==0)
+
+        # Assert that output is consistent with reference
+        out_ref = '''
+Extrapolating from VMC and DMC densities...
+
+Norm:   tot             = 7.999999969999998
+
+Non-Cumulative Value of C Species at Cutoff 0.6 is: 4.910093964664309
+'''
+        assert(text_eq(out,out_ref))
+
+        # DMC extrapolated cumulative
+        command = '{0} -s C -r 0.6 -c --vmc={1}/vmc.avg.s000.SpinDensity_u+d.xsf {2}/dmc.avg.s001.SpinDensity_u+d.xsf'.format(exe,vmc_path,dmc_path)
+        out,err,rc = execute(command)
+
+        # Assert that return code is 0
+        assert(rc==0)
+
+        # Assert that output is consistent with reference
+        out_ref = '''
+Extrapolating from VMC and DMC densities...
+
+Norm:   tot             = 7.999999969999998
+
+Cumulative Value of C Species at Cutoff 0.6 is: 1.1078267486386275
+'''
+        assert(text_eq(out,out_ref))
+
+
+        # DMC extrapolated cumulative with error bar
+        command = '{0} -s C -r 0.6 -c -n 3 --seed=0 --vmc={1}/vmc.avg.s000.SpinDensity_u+d.xsf --vmcerr={1}/vmc.avg.s000.SpinDensity_u+d+err.xsf --dmcerr={2}/dmc.avg.s001.SpinDensity_u+d+err.xsf {2}/dmc.avg.s001.SpinDensity_u+d.xsf'.format(exe,vmc_path,dmc_path)
+        out,err,rc = execute(command)
+
+        # Assert that return code is 0
+        assert(rc==0)
+
+        # Assert that output is consistent with reference
+        out_ref = '''
+Extrapolating from VMC and DMC densities...
+Resampling to obtain error bar (NOTE: This can be slow)...
+Will compute 3 samples...
+sample: 0
+sample: 1
+sample: 2
+
+Norm:   tot             = 7.999999969999998
+
+Cumulative Value of C Species at Cutoff 0.6 is: 1.1078267486386275+/-0.0016066467833404942
+'''
+        assert(text_eq(out,out_ref))
+    #end def test_radial_density
+#end if