Added and modified examples

examples/benzene_2p/parameters.py

@@ -0,0 +1,271 @@
+#! /usr/bin/env python3
+
+# Benzene (2 parameters; CC/CH)
+# 
+# This is an example of configuring the structural mappings and computing jobs based on the original publication
+# The file is not (yet) fully curated for pedagogical purposes, and may not reflect the latest good practices of composing the parameter file.
+# However, it serves to demonstrate that the implementation in parameters.py can be done in any almost any style, as long as it defines
+#   Starting structure (pos_init as 1D array)
+#   Consistent parameter mappings: (pos_to_params, params_to_pos)
+#   Functions returning Nexus workflows (get_relax_job,get_scf_pes_job,get_scf_ls_job,get_dmc_jobs)
+
+from numpy import array,sin,cos,pi,diag,linalg
+from nexus import generate_pwscf,generate_pw2qmcpack,generate_qmcpack,job,obj,Structure,generate_physical_system
+
+from surrogate_defaults import *
+from surrogate_tools import read_geometry
+
+# Structure
+label      = 'benzene'
+cell_init  = array([20.0,20.0,10.0])
+pos_xyz    = '''
+C  0.          2.65075664  0.
+H  0.          4.70596609  0.
+C -2.29562041  1.32537832  0.
+H -4.07549676  2.35299249  0.
+C -2.29562041 -1.32537832  0.
+H -4.07549676 -2.3529925   0.
+C  0.         -2.65075664  0.
+H  0.         -4.70596609  0.
+C  2.29562041 -1.32537832  0.
+H  4.07549676 -2.3529925   0.
+C  2.29562041  1.32537832  0.
+H  4.07549676  2.35299249  0.
+'''
+dim           = 3
+pos_init,elem = read_geometry(pos_xyz)
+pos_init      = (pos_init.reshape(-1,3) + cell_init/2).reshape(-1) # add cell
+masses        = 6*[10947.356792250725,918.68110941480279]
+relax_cell    = False
+num_prt       = len(elem)
+
+structure_input = obj(
+    dim    = 3,
+    elem   = elem,
+    units  = 'B',
+    kgrid  = (1,1,1),
+    kshift = (0,0,0),
+    )
+
+# param 1: CC distance (no shift H)
+r_CC = array([cos( 3*pi/6), sin( 3*pi/6), 0., 0., 0., 0.,
+              cos( 5*pi/6), sin( 5*pi/6), 0., 0., 0., 0.,
+              cos( 7*pi/6), sin( 7*pi/6), 0., 0., 0., 0.,
+              cos( 9*pi/6), sin( 9*pi/6), 0., 0., 0., 0.,
+              cos(11*pi/6), sin(11*pi/6), 0., 0., 0., 0.,
+              cos(13*pi/6), sin(13*pi/6), 0., 0., 0., 0.,])/6
+# param 2 : CH distance
+r_CH = array([-cos( 3*pi/6), -sin( 3*pi/6), 0.,cos( 3*pi/6), sin(3*pi/6), 0.,
+              -cos( 5*pi/6), -sin( 5*pi/6), 0.,cos( 5*pi/6), sin(5*pi/6), 0.,
+              -cos( 7*pi/6), -sin( 7*pi/6), 0.,cos( 7*pi/6), sin(7*pi/6), 0.,
+              -cos( 9*pi/6), -sin( 9*pi/6), 0.,cos( 9*pi/6), sin(9*pi/6), 0.,
+              -cos(11*pi/6), -sin(11*pi/6), 0.,cos(11*pi/6),sin(11*pi/6), 0.,
+              -cos(13*pi/6), -sin(13*pi/6), 0.,cos(13*pi/6),sin(13*pi/6), 0.,])/6
+r_HH = array([0., 0., 0.,cos( 3*pi/6), sin(3*pi/6), 0.,
+              0., 0., 0.,cos( 5*pi/6), sin(5*pi/6), 0.,
+              0., 0., 0.,cos( 7*pi/6), sin(7*pi/6), 0.,
+              0., 0., 0.,cos( 9*pi/6), sin(9*pi/6), 0.,
+              0., 0., 0.,cos(11*pi/6),sin(11*pi/6), 0.,
+              0., 0., 0.,cos(13*pi/6),sin(13*pi/6), 0.,])/6
+#delta_pinv = array([r_CC,r_HH])
+delta_pinv = array([r_CC,r_CH])
+delta      = linalg.pinv(delta_pinv)
+
+def pos_to_params(pos):
+    params = delta_pinv @ pos
+    return params
+#end def
+
+def params_to_pos(params):
+    #pos = delta @ params
+    pos = ((delta @ params).reshape(-1,3) + cell_init/2).flatten()
+    return pos
+#end def
+
+# Pseudos
+valences       = obj(C=4,H=1)
+relaxpseudos   = ['C.pbe_v1.2.uspp.F.UPF', 'H.pbe_v1.4.uspp.F.UPF']
+qmcpseudos     = ['C.ccECP.xml','H.ccECP.xml']
+scfpseudos     = ['C.upf','H.upf']
+
+# Setting for the nexus jobs based on file layout and computing environment
+pseudo_dir = '../pseudos'
+nx_machine = 'ws8'
+cores      = 8
+presub     = ''
+qmcapp     = '/path/to/qmcpack'
+qeapp      = '/path/to/pw.x'
+p2qapp     = '/path/to/pw2qmcpack.x'
+scfjob     = obj(app=qeapp, cores=cores,ppn=cores,presub=presub,hours=2)
+optjob     = obj(app=qmcapp,cores=cores,ppn=cores,presub=presub,hours=12)
+dmcjob     = obj(app=qmcapp,cores=cores,ppn=cores,presub=presub,hours=12)
+p2qjob     = obj(app=p2qapp,cores=1,ppn=1,presub=presub,minutes=5)
+
+scf_common = obj(
+    input_dft   = 'pbe',
+    occupations = None,
+    nosym       = False,
+    conv_thr    = 1e-9,
+    mixing_beta = .7,
+    )
+scf_relax_inputs = obj(
+    identifier    = 'relax',
+    input_type    = 'relax',
+    forc_conv_thr = 1e-4,
+    pseudos       = relaxpseudos,
+    ecut          = 100,
+    ecutrho       = 300,
+    **scf_common,
+    )
+scf_pes_inputs = obj(
+    identifier = 'scf',
+    input_type = 'scf',
+    pseudos    = relaxpseudos,
+    ecut       = 100,
+    ecutrho    = 300,
+    disk_io    = 'none',
+    **scf_common,
+    )
+scf_ls_inputs = obj(
+    identifier = 'scf',
+    input_type = 'scf',
+    pseudos    = scfpseudos,
+    ecut       = 300,
+    ecutrho    = 2000,
+    **scf_common,
+    )
+opt_inputs = obj(
+    identifier   = 'opt',
+    qmc          = 'opt',
+    input_type   = 'basic',
+    pseudos      = qmcpseudos,
+    bconds       = 'nnn',
+    J2           = True,
+    J1_size      = 6,
+    J1_rcut      = 6.0,
+    J2_size      = 6,
+    J2_rcut      = 6.0,
+    minmethod    = 'oneshift',
+    blocks       = 512,
+    substeps     = 2,
+    steps        = 1,
+    samples      = 128000,
+    minwalkers   = 0.05,
+    nonlocalpp   = True,
+    use_nonlocalpp_deriv = False,
+    )
+dmc_inputs = obj(
+    identifier   = 'dmc',
+    qmc          = 'dmc',
+    input_type   = 'basic',
+    pseudos      = qmcpseudos,
+    bconds       = 'nnn',
+    jastrows     = [],
+    vmc_samples  = 2000,
+    blocks       = 200,
+    timestep     = 0.01,
+    nonlocalmoves= True,
+    ntimesteps   = 1,
+    )
+nx_settings = obj(
+    sleep         = 3,
+    pseudo_dir    = pseudo_dir,
+    runs          = '',
+    results       = '',
+    status_only   = 0,
+    generate_only = 0,
+    account       = nx_account,
+    machine       = nx_machine,
+    )
+
+
+# construct system based on position
+def get_system(pos,cell=cell_init):
+    structure = Structure(
+        pos    = pos.reshape((-1,dim)),
+        axes   = diag(cell),
+        **structure_input,
+        )
+    return generate_physical_system(structure=structure,**valences)
+#end def
+
+def get_relax_job(pos,pstr,**kwargs):
+    relax     = generate_pwscf(
+        system = get_system(pos),
+        job    = job(**scfjob),
+        path   = pstr,
+        **scf_relax_inputs
+        )
+    return [relax]
+#end def
+
+# settings for the PES sweep
+def get_scf_pes_job(pos,path,**kwargs):
+    scf = generate_pwscf(
+        system     = get_system(pos),
+        job        = job(**scfjob),
+        path       = path,
+        **scf_pes_inputs,
+        )
+    return [scf]
+#end def
+
+# settings for the SCF ls
+def get_scf_ls_job(pos,path,**kwargs):
+    scf = generate_pwscf(
+        system     = get_system(pos),
+        job        = job(**scfjob),
+        path       = path,
+        **scf_ls_inputs,
+        )
+    return [scf]
+#end def
+
+# DMC line search
+steps_times_error2 = 4.8e-05 # (steps-1)* error**2
+def get_dmc_jobs(pos,path,sigma,jastrow=None,**kwargs):
+    system   = get_system(pos)
+    dmcsteps = int(steps_times_error2/sigma**2)+1
+
+    scf = generate_pwscf(
+        system     = system,
+        job        = job(**scfjob),
+        path       = path+'/scf',
+        **scf_ls_inputs,
+        )
+
+    p2q = generate_pw2qmcpack(
+        identifier   = 'p2q',
+        path         = path+'/scf',
+        job          = job(**p2qjob),
+        dependencies = [(scf,'orbitals')],
+        )
+
+    system.bconds = 'nnn'
+    if jastrow is None:
+        opt_cycles = 16
+    else:
+        opt_cycles = 8
+    #end if
+    opt = generate_qmcpack(
+        system       = system,
+        path         = path+'/opt',
+        job          = job(**optjob),
+        dependencies = [(p2q,'orbitals')],
+        cycles       = opt_cycles,
+        **opt_inputs
+        )
+    if not jastrow is None:
+        opt.depends((jastrow,'jastrow'))
+    #end if
+
+    dmc = generate_qmcpack(
+        system       = system,
+        path         = path+'/dmc',
+        job          = job(**dmcjob),
+        dependencies = [(p2q,'orbitals'),(opt,'jastrow') ],
+        steps        = dmcsteps,
+        **dmc_inputs
+        )
+    return [scf,p2q,opt,dmc]
+#end def

examples/coronene/parameters.py → examples/coronene_6p/parameters.py

@@ -1,5 +1,14 @@
 #! /usr/bin/env python3
 
+# Coronene (6 parameters)
+#
+# This is an example of configuring the structural mappings and computing jobs based on the original publication
+# The file is not (yet) fully curated for pedagogical purposes, and may not reflect the latest good practices of composing the parameter file.
+# However, it serves to demonstrate that the implementation in parameters.py can be done in any almost any style, as long as it defines
+#   Starting structure (pos_init as 1D array)
+#   Consistent parameter mappings: (pos_to_params, params_to_pos)
+#   Functions returning Nexus workflows (get_relax_job,get_scf_pes_job,,get_dmc_jobs)
+
 from numpy import array,diag,linalg,sin,cos,pi,arcsin,arccos
 from nexus import generate_pwscf,generate_pw2qmcpack,generate_qmcpack,job,obj,Structure,generate_physical_system
 
@@ -147,36 +156,25 @@ def rotate_xy(angle):
     return pos
 #end def
 
-# jobs
+# Pseudos
 valences       = obj(C=4,H=1)
 relaxpseudos   = ['C.pbe_v1.2.uspp.F.UPF', 'H.pbe_v1.4.uspp.F.UPF']
 qmcpseudos     = ['C.ccECP.xml','H.ccECP.xml']
 scfpseudos     = ['C.upf','H.upf']
-steps_times_error2 = 0.0003 # (steps-1)* error**2
 
-# setting for the surrogate job
+# Setting for the nexus jobs based on file layout and computing environment
 pseudo_dir = '../pseudos'
-nx_account = 'qmc'
-nx_machine = 'cades'
-cores      = 36
-presub = '''
-export OMP_NUM_THREADS=1
-module purge
-module load python/3.6.3
-module load PE-intel/3.0
-module load intel/18.0.0
-module load gcc/6.3.0
-module load hdf5_parallel/1.8.17
-module load fftw/3.3.5
-module load cmake
-module load boost/1.67.0
-module load libxml2/2.9.9
-'''
-qmcapp = '/home/49t/git/qmcpack/latest/build_cades_cpu_real_skylake/bin/qmcpack'
-scfjob = obj(app='pw.x',cores=cores,ppn=cores,presub=presub,hours=2,queue='burst')
-optjob = obj(app=qmcapp,cores=cores,ppn=cores,presub=presub,hours=12)
-dmcjob = obj(app=qmcapp,cores=cores,ppn=cores,presub=presub,hours=12)
-p2qjob = obj(app='pw2qmcpack.x',cores=1,ppn=1,presub=presub,minutes=5,queue='burst')
+nx_machine = 'ws8'
+cores      = 8
+presub     = ''
+qmcapp     = '/path/to/qmcpack'
+qeapp      = '/path/to/pw.x'
+p2qapp     = '/path/to/pw2qmcpack.x'
+scfjob     = obj(app=qeapp, cores=cores,ppn=cores,presub=presub,hours=2)
+optjob     = obj(app=qmcapp,cores=cores,ppn=cores,presub=presub,hours=12)
+dmcjob     = obj(app=qmcapp,cores=cores,ppn=cores,presub=presub,hours=12)
+p2qjob     = obj(app=p2qapp,cores=1,ppn=1,presub=presub,minutes=5)
+
 
 scf_common = obj(
     input_dft   = 'pbe',
@@ -296,6 +294,7 @@ def get_scf_pes_job(pos,path,**kwargs):
 #end def
 
 # DMC line search
+steps_times_error2 = 0.0003 # (steps-1)* error**2
 def get_dmc_jobs(pos,path,sigma,jastrow=None,**kwargs):
     system   = get_system(pos)
     dmcsteps = int(steps_times_error2/sigma**2)+1