champ module
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../../data/module_gitignore
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10
README.md
10
README.md
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# qp_plugins_scemama
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# qp_plugins
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Programs developed for the [Quantum Package](http://github.com/LCPQ/quantum_package).
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* `/stable` : Plugins that are stable and maintained
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* `/devel` : Experimental plugins under development
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* `/deprecated` : Old plugins that have been abandoned and are not maintained
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Programs developed for the [Quantum Package](http://github.com/LCPQ/qp2).
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[ci_threshold]
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type: Threshold
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doc: Threshold on the CI coefficients
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interface: ezfio,provider,ocaml
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default: 1.e-8
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determinants fci
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===============
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CHAMP Interface
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===============
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Interface from Quantum Package to
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[CHAMP](https://www.utwente.nl/en/tnw/ccp/research/CHAMP.html).
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For multi-state calculations, to extract state 2 use:
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.. code-block:: bash
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QP_STATE=2 qp_run save_for_champ x.ezfio
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(state 1 is the ground state).
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#!/usr/bin/env python2
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#
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# Modified from the QMCPACK interface developed by @tapplencourt and @abenali
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print "#QP -> CHAMP"
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# ___
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# | ._ o _|_
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# _|_ | | | |_
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#
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from ezfio import ezfio
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import os
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import sys
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ezfio_path = sys.argv[1]
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ezfio.set_file(ezfio_path)
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do_pseudo = ezfio.get_pseudo_do_pseudo()
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if do_pseudo:
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print "do_pseudo True"
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from qp_path import QP_ROOT
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l_ele_path = os.path.join(QP_ROOT,"data","list_element.txt")
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with open(l_ele_path, "r") as f:
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data_raw = f.read()
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l_element_raw = data_raw.split("\n")
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l_element = [element_raw.split() for element_raw in l_element_raw]
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d_z = dict((abr, z) for (z, abr, ele, _) in filter(lambda x: x != [], l_element) )
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else:
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print "do_pseudo False"
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try:
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n_det = ezfio.get_determinants_n_det()
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except IOError:
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n_det = 1
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if n_det == 1:
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print "multi_det False"
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else:
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print "multi_det True"
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#
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# |\/| o _ _
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# | | | _> (_
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#
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def list_to_string(l):
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return " ".join(map(str, l))
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ao_num = ezfio.get_ao_basis_ao_num()
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print "ao_num", ao_num
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mo_num = ezfio.get_mo_basis_mo_num()
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print "mo_num", mo_num
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alpha = ezfio.get_electrons_elec_alpha_num()
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beta = ezfio.get_electrons_elec_beta_num()
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print "elec_alpha_num", alpha
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print "elec_beta_num", beta
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print "elec_tot_num", alpha + beta
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print "spin_multiplicity", (alpha - beta) + 1
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l_label = ezfio.get_nuclei_nucl_label()
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l_charge = ezfio.get_nuclei_nucl_charge()
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l_coord = ezfio.get_nuclei_nucl_coord()
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l_coord_str = [list_to_string(i) for i in zip(*l_coord)]
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print "nucl_num", len(l_label)
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# _
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# / _ _ ._ _|
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# \_ (_) (_) | (_|
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#
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print "Atomic coord in Bohr"
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for i, t in enumerate(zip(l_label, l_charge, l_coord_str)):
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t_1 = d_z[t[0]] if do_pseudo else t[1]
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t_new = [t[0],t_1,t[2]]
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print list_to_string(t_new)
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#
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# Call externet process to get the sysmetry
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#
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import subprocess
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process = subprocess.Popen(
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['qp_print_basis', ezfio_path],
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stdout=subprocess.PIPE)
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out, err = process.communicate()
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basis_raw, sym_raw, _ = out.split("\n\n\n")
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# _ __
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# |_) _. _ o _ (_ _ _|_
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# |_) (_| _> | _> __) (/_ |_
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#
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basis_without_header = "\n".join(basis_raw.split("\n")[11:])
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import re
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l_basis_raw = re.split('\n\s*\n', basis_without_header)
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a_already_print = []
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l_basis_clean = []
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for i, (a,b) in enumerate(zip(l_label,l_basis_raw)):
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if a not in a_already_print:
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l_basis_clean.append(b.replace('Atom {0}'.format(i + 1), a))
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a_already_print.append(a)
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else:
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continue
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print "BEGIN_BASIS_SET\n"
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print "\n\n".join(l_basis_clean)
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print "END_BASIS_SET"
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# _
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# |\/| / \ _
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# | | \_/ _>
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#
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#
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# Function
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#
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d_gms_order ={ 0:["s"],
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1:[ "x", "y", "z" ],
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2:[ "xx", "yy", "zz", "xy", "xz", "yz" ],
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3:[ "xxx", "yyy", "zzz", "xxy", "xxz", "yyx", "yyz", "zzx", "zzy", "xyz"],
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4:[ "xxxx", "yyyy", "zzzz", "xxxy", "xxxz", "yyyx", "yyyz", "zzzx", "zzzy", "xxyy", "xxzz", "yyzz", "xxyz", "yyxz", "zzxy"] }
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def compare_gamess_style(item1, item2):
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n1,n2 = map(len,(item1,item2))
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assert (n1 == n2)
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try:
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l = d_gms_order[n1]
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except KeyError:
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return 0
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# raise (KeyError, "We dont handle L than 4")
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else:
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a = l.index(item1)
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b = l.index(item2)
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return cmp( a, b )
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def expend_sym_str(str_):
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#Expend x2 -> xx
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# yx2 -> xxy
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for i, c in enumerate(str_):
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try:
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n = int(c)
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except ValueError:
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pass
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else:
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str_ = str_[:i - 1] + str_[i - 1] * n + str_[i + 1:]
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#Order by frequency
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return "".join(sorted(str_, key=str_.count, reverse=True))
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def expend_sym_l(l_l_sym):
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for l in l_l_sym:
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l[2] = expend_sym_str(l[2])
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return l_l_sym
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def n_orbital(n):
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if n==0:
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return 1
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elif n==1:
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return 3
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else:
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return 2*n_orbital(n-1)-n_orbital(n-2)+1
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def get_nb_permutation(str_):
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if (str_) == 's': return 1
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else: return n_orbital(len(str_))
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def order_l_l_sym(l_l_sym):
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n = 1
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iter_ = range(len(l_l_sym))
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for i in iter_:
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if n != 1:
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n += -1
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continue
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l = l_l_sym[i]
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n = get_nb_permutation(l[2])
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l_l_sym[i:i + n] = sorted(l_l_sym[i:i + n],
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key=lambda x: x[2],
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cmp=compare_gamess_style)
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return l_l_sym
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#==========================
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# We will order the symetry
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#==========================
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l_sym_without_header = sym_raw.split("\n")[3:-2]
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l_l_sym_raw = [i.split() for i in l_sym_without_header]
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l_l_sym_expend_sym = expend_sym_l(l_l_sym_raw)
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l_l_sym_ordered = order_l_l_sym(l_l_sym_expend_sym)
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#========
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#MO COEF
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#========
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def order_phase(mo_coef):
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#Order
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mo_coef_phase = []
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import math
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for i in mo_coef:
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if abs(max(i)) > abs(min(i)):
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sign_max = math.copysign(1, max(i))
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else:
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sign_max = math.copysign(1, min(i))
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if sign_max == -1:
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ii = [-1 * l for l in i]
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else:
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ii = i
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mo_coef_phase.append(ii)
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return mo_coef_phase
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def chunked(l, chunks_size):
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l_block = []
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for i in l:
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chunks = [i[x:x + chunks_size] for x in xrange(0, len(i), chunks_size)]
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l_block.append(chunks)
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return l_block
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def print_mo_coef(mo_coef_block, l_l_sym):
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print ""
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print "BEGIN_MO"
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print ""
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len_block_curent = 0
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nb_block = len(mo_coef_block[0])
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for i_block in range(0, nb_block):
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a = [i[i_block] for i in mo_coef_block]
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r_ = range(len_block_curent, len_block_curent + len(a[0]))
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print " ".join([str(i + 1) for i in r_])
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len_block_curent += len(a[0])
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for l in l_l_sym:
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i = int(l[0]) - 1
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i_a = int(l[1]) - 1
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sym = l[2]
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print l_label[i_a], sym, " ".join('%20.15e'%i
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for i in a[i])
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if i_block != nb_block - 1:
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print ""
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else:
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print "END_MO"
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mo_coef = ezfio.get_mo_basis_mo_coef()
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mo_coef_transp = zip(*mo_coef)
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mo_coef_block = chunked(mo_coef_transp, 4)
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print_mo_coef(mo_coef_block, l_l_sym_ordered)
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# _
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# |_) _ _ _| _
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# | _> (/_ |_| (_| (_)
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#
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if do_pseudo:
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print ""
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print "BEGIN_PSEUDO"
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klocmax = ezfio.get_pseudo_pseudo_klocmax()
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kmax = ezfio.get_pseudo_pseudo_kmax()
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lmax = ezfio.get_pseudo_pseudo_lmax()
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n_k = ezfio.get_pseudo_pseudo_n_k()
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v_k = ezfio.get_pseudo_pseudo_v_k()
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dz_k = ezfio.get_pseudo_pseudo_dz_k()
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n_kl = ezfio.get_pseudo_pseudo_n_kl()
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v_kl = ezfio.get_pseudo_pseudo_v_kl()
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dz_kl = ezfio.get_pseudo_pseudo_dz_kl()
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for i, a in enumerate(l_label):
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l_str = []
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#Local
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l_dump = []
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for k in range(klocmax):
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if v_k[k][i]:
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l_ = list_to_string([v_k[k][i], n_k[k][i] + 2, dz_k[k][i]])
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l_dump.append(l_)
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l_str.append(l_dump)
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#Non local
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for l in range(lmax + 1):
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l_dump = []
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for k in range(kmax):
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if v_kl[l][k][i]:
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l_ = list_to_string([v_kl[l][k][i], n_kl[l][k][i] + 2,
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dz_kl[l][k][i]])
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l_dump.append(l_)
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if l_dump:
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l_str.append(l_dump)
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str_ = "PARAMETERS FOR {0} ON ATOM {1} WITH ZCORE {2} AND LMAX {3} ARE"
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print str_.format(a, i + 1, int(d_z[a])-int(l_charge[i]), int(len(l_str) - 1))
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for i, l in enumerate(l_str):
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str_ = "FOR L= {0} COEFF N ZETA"
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print str_.format(int(len(l_str) - i - 1))
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for ii, ll in enumerate(l):
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print " ", ii + 1, ll
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str_ = "THE ECP RUN REMOVES {0} CORE ELECTRONS, AND THE SAME NUMBER OF PROTONS."
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print str_.format(sum([int(d_z[a])-int(l_charge[i]) for i,a in enumerate(l_label)]))
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print "END_PSEUDO"
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# _
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# | \ _ _|_
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# |_/ (/_ |_
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#
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psi_coef = ezfio.get_determinants_psi_coef()
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psi_det = ezfio.get_determinants_psi_det()
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bit_kind = ezfio.get_determinants_bit_kind()
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nexcitedstate = ezfio.get_determinants_n_states()
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print ""
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print "BEGIN_DET"
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print ""
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print "mo_num", mo_num
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print "det_num", n_det
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print ""
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if "QP_STATE" in os.environ:
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state = int(os.environ["QP_STATE"])-1
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else:
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state = 0
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psi_coef_small = psi_coef[state]
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encode = 8*bit_kind
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def bindigits(n, bits):
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s = bin(n & int("1"*bits, 2))[2:]
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return ("{0:0>%s}" % (bits)).format(s)
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decode = lambda det: ''.join(bindigits(i,encode)[::-1] for i in det)[:mo_num]
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MultiDetAlpha = []
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MultiDetBeta = []
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for coef, (det_a, det_b) in zip(psi_coef_small, psi_det):
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print coef
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MyDetA=decode(det_a)
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MyDetB=decode(det_b)
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print MyDetA
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print MyDetB
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print ''
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MultiDetAlpha.append( det_a )
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MultiDetBeta.append( det_b )
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print "END_DET"
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@ -0,0 +1,25 @@
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program qmcpack
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implicit none
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BEGIN_DOC
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! Generates a file for QMCPACK
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END_DOC
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integer :: i,j
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read_wf = .True.
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TOUCH read_wf
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do j=1,ao_prim_num_max
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do i=1,ao_num
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ao_coef(i,j) = ao_coef(i,j) * ao_coef_normalization_factor(i)
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enddo
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enddo
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call ezfio_set_ao_basis_ao_coef(ao_coef)
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do j=1,mo_num
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do i=1,ao_num
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mo_coef(i,j) *= 1.d0/ao_coef_normalization_factor(i)
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enddo
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enddo
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call save_mos
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call system('rm '//trim(ezfio_filename)//'/mo_basis/ao_md5')
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call system('$QP_ROOT/src/champ/qp_convert.py '//trim(ezfio_filename))
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end
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