Merge branch 'develop' into add_dense_hamiltonian

nexus/lib/gamess.py

@@ -32,12 +32,13 @@
 
 
 import os
+import numpy as np
 from numpy import array,ndarray,abs
 from generic import obj
 from developer import DevBase
 from debug import *
 from simulation import Simulation
-from gamess_input import GamessInput,generate_gamess_input,FormattedGroup,KeywordGroup,GuessGroup
+from gamess_input import GamessInput,generate_gamess_input,FormattedGroup,KeywordGroup,GuessGroup,GIarray
 from gamess_analyzer import GamessAnalyzer
 
 
@@ -67,6 +68,16 @@ def restore_default_settings():
     #end def restore_default_settings
 
 
+    def __init__(self,**kwargs):
+        self.mo_reorder = None
+        mo_reorder = kwargs.pop('mo_reorder',None)
+        if mo_reorder is not None:
+            self.mo_reorder = [s.lower() for s in mo_reorder]
+        #end if
+        Simulation.__init__(self,**kwargs)
+    #end def __init__
+
+
     def init_job_extra(self):
         # gamess seems to need lots of environment variables to run properly
         # nearly all of these are names of output/work files
@@ -114,6 +125,9 @@ def get_result(self,result_name,sim):
                 result.norbitals = analyzer.punch.norbitals
                 result.vec       = analyzer.punch.vec
             #end if
+            if 'orbitals' in analyzer:
+                result.orbitals = analyzer.orbitals
+            #end if
         else:
             self.error('ability to get result '+result_name+' has not been implemented')
         #end if
@@ -135,7 +149,64 @@ def incorporate_result(self,result_name,result,sim):
             else:
                 norb = result.norbitals
             #end if
-            input.guess.clear()
+            if 'norder' not in input.guess:
+                input.guess.clear()
+            #end if
+            if self.mo_reorder is not None:
+                if 'orbitals' not in result:
+                    self.error('Orbital information from prior calculation "{}" located at {} cannot be found. You requested orbital reordering via the  "mo_reorder" input keyword.  Due to missing information, this operation cannot be performed.  The current simulation "{}" is located at {}.'.format(sim.identifier,sim.locdir,self.identifier,self.locdir))
+                    self.block()
+                #end if
+                guess_inputs = obj()
+                ecounts = self.system.particles.electron_counts()
+                orbs = result.orbitals
+                order_map = obj(up='iorder',down='jorder')
+                nelec_map = obj(up=ecounts[0],down=ecounts[1])
+                for spin,vname in order_map.items():
+                    nelec = nelec_map[spin]
+                    if len(self.mo_reorder)<nelec:
+                        self.error('Too few symmetries provided in "mo_reorder" for spin "{0}".\nNumber of electrons with spin "{0}": {1}\nNumber of entries in "mo_reorder": {2}\nContents of "mo_reorder": {3}\nSimulation identifier: {4}\nSimulation location: {5}'.format(spin,nelec,len(self.mo_reorder),self.mo_reorder,self.identifier,self.locdir))
+                    #end if
+                    symmetries = [s.lower() for s in orbs[spin].symmetry]
+                    missing = set(self.mo_reorder)-set(symmetries)
+                    if len(missing)>0:
+                        self.error('Symmetries provided by "mo_reorder" keyword are not found in the outputted MOs.\nSet of symmetries provided in "mo_reorder": {}\nSet of symmetries present in MOs: {}\nContents of "mo_reorder": {}\nSimulation identifier: {}\nSimulation location: {}'.format(sorted(set(self.mo_reorder)),sorted(set(symmetries)),self.mo_reorder,self.identifier,self.locdir))
+                    #end if
+                    occ  = np.zeros(len(symmetries),dtype=bool)
+                    for symm in self.mo_reorder[:nelec]:
+                        for i,(s,o) in enumerate(zip(symmetries,occ)):
+                            if not o and symm==s:
+                                occ[i] = True
+                                break
+                            #end if
+                        #end for
+                    #end for
+                    if occ.sum()<nelec:
+                        self.error('Too few orbitals occupied based on "mo_reorder" request.\nNumber of orbitals occupied: {}\nNumber of spin "{}" electrons: {}\nContents of "mo_reorder": {}\nSimulation identifier: {}\nSimulation location: {}'.format(occ.sum(),spin,nelec,self.mo_reorder,self.identifier,self.locdir))
+                    #end if
+                    indices = np.arange(len(symmetries),dtype=int)[occ]+1
+                    start = 0
+                    found = False
+                    for i in range(len(indices)):
+                        start = i
+                        if indices[i]!=i+1:
+                            found = True
+                            break
+                        #end if
+                    #end if
+                    if found:
+                        reduced_indices = indices[start:]
+                        start+=1
+                    else:
+                        reduced_indices = []
+                    #end if
+                    if len(reduced_indices)>0:
+                        guess_inputs.norder = 1
+                        guess_inputs[vname] = GIarray({start:reduced_indices})
+                    #end if
+                #end for
+                input.guess.set(**guess_inputs)
+            #end if
             input.guess.set(
                 guess = 'moread',
                 norb  = norb,
@@ -194,7 +265,7 @@ def output_filepath(self,name):
 
 
 def generate_gamess(**kwargs):
-    sim_args,inp_args = Gamess.separate_inputs(kwargs,copy_pseudos=False)
+    sim_args,inp_args = Gamess.separate_inputs(kwargs,copy_pseudos=False,sim_kw=['mo_reorder'])
 
     if not 'input' in sim_args:
         sim_args.input = generate_gamess_input(**inp_args)

nexus/lib/gamess_analyzer.py

@@ -167,7 +167,7 @@ def analyze_log(self):
         #end if
 
         # try to get the up/down orbitals
-        if 'counts' in self and False: # don't read orbitals, large
+        if 'counts' in self:
             orbitals = obj()
             try:
                 self.read_orbitals(log,orbitals,'up'  ,'-- ALPHA SET --')
@@ -264,39 +264,43 @@ def read_orbitals(self,log,orbs,spec,header):
                 #end if
                 eigenvalue.extend(log.readtokens())
                 symmetry.extend(log.readtokens())
-                coeff = []
+                # skip large coefficient data
                 for icao in xrange(cao_tot):
-                    tokens = log.readtokens()
-                    if not have_basis:
-                        e = tokens[1]
-                        element.append(e[0].upper()+e[1:].lower())
-                        spec_index.append(tokens[2])
-                        angular.append(tokens[3])
-                    #end if
-                    coeff.append(tokens[4:])
+                    log.readline()
                 #end for
-                coefficients.extend(array(coeff,dtype=float).T)
-                if not have_basis:
-                    stype = []
-                    ptype = []
-                    dtype = []
-                    ftype = []
-                    for ia in xrange(len(angular)):
-                        a = angular[ia].lower()
-                        if a in GamessAnalyzer.stypes:
-                            stype.append(ia)
-                        elif a in GamessAnalyzer.ptypes:
-                            ptype.append(ia)
-                        elif a in GamessAnalyzer.dtypes:
-                            dtype.append(ia)
-                        elif a in GamessAnalyzer.ftypes:
-                            ftype.append(ia)
-                        elif self.info.exit:
-                            self.error('unrecognized angular type: {0}'.format(angular[ia]))
-                        #end if
-                    #end for
-                #end if
-                have_basis = True
+                #coeff = []
+                #for icao in xrange(cao_tot):
+                #    tokens = log.readtokens()
+                #    if not have_basis:
+                #        e = tokens[1]
+                #        element.append(e[0].upper()+e[1:].lower())
+                #        spec_index.append(tokens[2])
+                #        angular.append(tokens[3])
+                #    #end if
+                #    coeff.append(tokens[4:])
+                ##end for
+                #coefficients.extend(array(coeff,dtype=float).T)
+                #if not have_basis:
+                #    stype = []
+                #    ptype = []
+                #    dtype = []
+                #    ftype = []
+                #    for ia in xrange(len(angular)):
+                #        a = angular[ia].lower()
+                #        if a in GamessAnalyzer.stypes:
+                #            stype.append(ia)
+                #        elif a in GamessAnalyzer.ptypes:
+                #            ptype.append(ia)
+                #        elif a in GamessAnalyzer.dtypes:
+                #            dtype.append(ia)
+                #        elif a in GamessAnalyzer.ftypes:
+                #            ftype.append(ia)
+                #        elif self.info.exit:
+                #            self.error('unrecognized angular type: {0}'.format(angular[ia]))
+                #        #end if
+                #    #end for
+                ##end if
+                #have_basis = True
                 mos_found = len(eigenvalue)
                 i+=1
             #end while
@@ -309,16 +313,17 @@ def read_orbitals(self,log,orbs,spec,header):
                 orbs[spec] = obj(
                     eigenvalue   = array(eigenvalue  ,dtype=float),
                     symmetry     = array(symmetry    ,dtype=str  ),
-                    coefficients = array(coefficients,dtype=float),
-                    basis = obj(
-                        element    = array(element   ,dtype=str),
-                        spec_index = array(spec_index,dtype=int),
-                        angular    = array(angular   ,dtype=str),
-                        stype      = array(stype     ,dtype=int),
-                        ptype      = array(ptype     ,dtype=int),
-                        dtype      = array(dtype     ,dtype=int),
-                        ftype      = array(ftype     ,dtype=int),
-                        )
+                    # skip large coefficient data
+                    #coefficients = array(coefficients,dtype=float),
+                    #basis = obj(
+                    #    element    = array(element   ,dtype=str),
+                    #    spec_index = array(spec_index,dtype=int),
+                    #    angular    = array(angular   ,dtype=str),
+                    #    stype      = array(stype     ,dtype=int),
+                    #    ptype      = array(ptype     ,dtype=int),
+                    #    dtype      = array(dtype     ,dtype=int),
+                    #    ftype      = array(ftype     ,dtype=int),
+                    #    )
                     )
             #end if
             return success

nexus/lib/simulation.py

@@ -284,14 +284,19 @@ def code_name(cls):
 
     # test needed
     @classmethod
-    def separate_inputs(cls,kwargs,overlapping_kw=-1,copy_pseudos=True):
+    def separate_inputs(cls,kwargs,overlapping_kw=-1,copy_pseudos=True,sim_kw=None):
         if overlapping_kw==-1:
             overlapping_kw = set(['system'])
         elif overlapping_kw is None:
             overlapping_kw = set()
         #end if
+        if sim_kw is None:
+            sim_kw = set()
+        else:
+            sim_kw = set(sim_kw)
+        #end if
         kw       = set(kwargs.keys())
-        sim_kw   = kw & Simulation.allowed_inputs
+        sim_kw   = kw & (Simulation.allowed_inputs | sim_kw)
         inp_kw   = (kw - sim_kw) | (kw & overlapping_kw)    
         sim_args = obj()
         inp_args = obj()

src/QMCTools/PyscfToQmcpack.py

@@ -517,7 +517,7 @@ def order_mo_coef(ll):
     GroupCell.create_dataset("LatticeVectors",(3,3),dtype="f8",data=loc_cell.lattice_vectors())
 
     def get_mo(mo_coeff, cart):
-        return order_mo_coef(mo_coeff) if cart else zip(*mo_coeff)
+        return order_mo_coef(mo_coeff) if cart else list(zip(*mo_coeff))
 
     #Supertwist Coordinate
     GroupDet.create_dataset("Coord",(1,3),dtype="f8",data=sp_twist)

tests/test_automation/nightly_anl_bora.sh

@@ -5,25 +5,31 @@
 # Run the "short" nightlies
 # 
 
+# load necessary modules
+source /etc/profile.d/z00_lmod.sh
+if [ -d /scratch/packages/modulefiles ]; then
+  module use /scratch/packages/modulefiles
+fi
+
+module load intel-mkl intel/18.4
+module load openmpi/4.0.2-intel
+module load cuda/10.1
+
 export TEST_SITE_NAME=bora.alcf.anl.gov
-export N_PROCS_BUILD=16
 export N_PROCS=16
+export N_PROCS_BUILD=16
+export N_CONCURRENT_TESTS=16
 export CC=mpicc
 export CXX=mpicxx
-export BOOST_ROOT=/sandbox/opt/boost_1_61_0
 
 # run on socket 1
 NUMA_ID=1
 
-#CUDA
-export PATH=/sandbox/opt/NVIDIA/cuda-10.0/bin:$PATH
-export LD_LIBRARY_PATH=/sandbox/opt/NVIDIA/cuda-10.0/lib64:$LD_LIBRARY_PATH
-
-QE_BIN=/sandbox/opt/qe-stable/qe-6.4.1/bin
-QMC_DATA=/sandbox/opt/h5data
+QE_BIN=/scratch/opt/qe-stable/qe-6.4.1/bin
+QMC_DATA=/scratch/opt/h5data
 
 #Must be an absolute path
-place=/sandbox/QMCPACK_CI_BUILDS_DO_NOT_REMOVE
+place=/scratch/QMCPACK_CI_BUILDS_DO_NOT_REMOVE
 
 #define and load compiler
 compiler=Intel2018