Adding nexus. (#197)

* Develop (#196) * Image augmentation. * Augment images. * Augment images. * Specie update. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Add Latt2D, STM image (b-1) fix, image augmentation fix. * Update conf.py * Update conf.py * Multi-output graph bacthing. * Add EDOS dataset. * Temp. * Add circuit maker. * Add circuit maker. * NELECT update. * Version update, more DBs added. * Fix CHGCAR vasp. * Added volumetric reshape for CHGCAR. * Tmp * Tershoff Hamman update, specie update. * Add crop from center in STM. * Add Fourier transfor in STM. * Update STM pytest. * Add DPI to STM. * Zeo++ added, Atoms cif update, STM update, random vacancy maker added. * Atoms tempfile fix, Potcar from atoms module added. * Test for docs. * C2DB link update, docs Atoms update. * C2DB link update, docs Atoms update. * Version update, COD DB, QM9 JCTC DB added. * Compostion bug fix, elemental descriptor added. * Develop (#186) * Update outputs.py I added the calculation of the Raman intensities inside parse_raman_dat * Update outputs.py * Update outputs.py * Update outputs.py * Update cfid.py * Delete __init__.py * stylecss added. * stylecss added. * Adding extra Makefile/ * Remove examples from docs. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Docs update. * Tutorials update. * Tutorials docs update. * Docs update,pdb reader updated. * Update action_build.yml * Update action_build.yml * Remove pytraj strong dependencies. * Update docs, Added PDBBind and HPOV datasets. * Docs update. * Add thcikness to surface builder. * Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix. * Typo fix. * Add names to chem descs. * Lessen hermsolver pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * Reduced pytest. * No DFT3D * Exclude dft_3d dataset for memory issue. * Update figshare test. * Update figshare test. * Exclude db from coverage. * Exclude db from coverage. * Add magpie.json. * Add magpie.json. * Wien2k bands bug fix. * Wien2k bands bug fix. * Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code. * JFF update. * Add JQE_TB3 and hMOF dataset. * Update LAMMPS module. * Update LAMMPS module. * Fix elastic tensor module. * Figshare update, docs db name update. * Substitutions. * Update figshare dft_3d, cfid_3d. * Docs data update. * Generate substitutions. * Lint fix. * Update DOS. * Update DOS. Co-authored-by: tavazza <tavazza@gmail.com> Co-authored-by: knc6 <kamal.choudhary@nist.gov> Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu> * First input. * added black * Example folder. Co-authored-by: Kamal Choudhary <writetokamal.1989@gmail.com> Co-authored-by: tavazza <tavazza@gmail.com> Co-authored-by: knc6 <kamal.choudhary@nist.gov> Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>
usnistgov · Dec 20, 2021 · 62a4abd · 62a4abd
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diff --git a/jarvis/io/nexus/examples/cubic_diamond/POSCAR b/jarvis/io/nexus/examples/cubic_diamond/POSCAR
@@ -0,0 +1,10 @@
+cubic diamond
+   5.5
+ 0.0    0.5     0.5
+ 0.5    0.0     0.5
+ 0.5    0.5     0.0
+Si
+  2
+Direct
+ -0.125 -0.125 -0.125
+  0.125  0.125  0.125
diff --git a/jarvis/io/nexus/examples/cubic_diamond/diamond-dft.py b/jarvis/io/nexus/examples/cubic_diamond/diamond-dft.py
@@ -0,0 +1,99 @@
+#! /usr/bin/env python
+
+from nexus import settings,job,run_project,obj
+from nexus import generate_physical_system
+from nexus import generate_pwscf, generate_pw2qmcpack
+from nexus import generate_qmcpack,vmc,loop,linear,dmc
+from nexus import read_structure
+from numpy import mod, sqrt, array
+from qmcpack_input import spindensity
+import numpy as np
+from structure import optimal_tilematrix
+from numpy.linalg import det
+settings(
+    results = './results',
+    pseudo_dir = './pseudopotentials', #location of pseudopotential directory
+    sleep   = 1,
+    runs    = './runs',
+    machine = 'kisir', #machine, defined in the machine.py file in Nexus lib
+    )
+
+structure = read_structure('POSCAR', format='poscar') #poscar to be read from JARVIS-ID
+
+boundaries = 'ppp'
+supercells = [[[1, 0, 0], [0, 1, 0], [0, 0, 1]]] #Matrix used to tile to different sized supercells in kspace (for finite-size convergence)
+
+shared_qe = obj(        #QE parameters, if desired can loop over values of ecut and kgrid to find converged values at this stage
+    occupations = 'smearing',
+    smearing    = 'gaussian',
+    degauss     = 0.005,
+    input_dft   = 'PBE',
+    ecut        = 100,
+    conv_thr    = 1.0e-7,
+    mixing_beta = 0.2,
+    nosym       = True,
+    use_folded  = True,
+    spin_polarized = True
+)
+
+qe_presub = 'module load intel impi openmpi-3.0.1/intel qe-6.4.1' #loaded module for QE, can modify this for NIST cluster 
+
+qe_job = job(nodes=2,threads=40,app='pw.x', presub=qe_presub) #submission details specific to kisir
+
+scales = [1.00] #can modify to scale the lattice 
+
+for scale in scales: 
+#Self-consistent DFT calculation to obtain charge density of structure in POSCAR
+    temp = structure.copy()
+    temp.stretch(scale, scale , scale)
+    system = generate_physical_system(
+        structure = temp,
+        Si = 4,  # This is number of valence electrons for each element 
+        kshift   = (0,0,0),
+        net_spin = 0
+    )
+
+    scf = generate_pwscf(
+        identifier = 'scf',                      # log output goes to scf.out
+        path       = 'scf-{}'.format(scale),      # directory to run in
+        job        = qe_job,
+        system     = system,
+        input_type = 'scf',
+        pseudos    = ['Si.ccECP.upf'], #DFT pseudopotential from the directory
+        kgrid      = (4,4,4),
+        wf_collect = False,
+        **shared_qe
+    )
+    #Nonself-consistent DFT calculation to read in charge density and tile to appropriate supercell for QMC
+    for supercell in supercells:
+        scell_vol = det(supercell)
+        nscf_kgrid_k = int(np.ceil(2/sqrt(scell_vol))) #The kgrid for the nscf calculation used to tile to different sized supercells, modify this based on system
+        nscf_grid = (nscf_kgrid_k, nscf_kgrid_k, nscf_kgrid_k)
+        nscf_system = generate_physical_system(
+            structure = temp,
+            Si = 4,
+            tiling = supercell,
+            kgrid  = nscf_grid,
+            kshift = (0,0,0),
+            net_spin = 0,
+        )
+        nscf = generate_pwscf(
+            identifier  = 'nscf',
+            path        = 'nscf-{}-{}'.format(scale,scell_vol),
+            job         = qe_job ,
+            system      = nscf_system,
+            input_type  = 'nscf',
+            pseudos     = ['Si.ccECP.upf'], #DFT pseudopotential from the directory
+            wf_collect   = True,
+            dependencies = (scf,'charge_density'),
+            **shared_qe
+            )
+#Wavefunction conversion (p2qmcpack.x run on top of pw.x in same folder as NSCF calculation)
+        p2q = generate_pw2qmcpack(
+            identifier   = 'p2q',
+            path         = 'nscf-{}-{}'.format(scale,scell_vol),
+            job          = job(cores= 1,threads= 1,app='pw2qmcpack.x',presub=qe_presub),
+            write_psir   = False,
+            dependencies = (nscf,'orbitals'),
+            )
+run_project()