def locate_ref_dmfile(path=None, filename="Densmat_SCF.txt", prop_key="HF_ref",
jsonfile="DMfinder.json", ccpfile="CCParser.json"):
"""
"""
path = ut.deal_with_type(path, condition=None, to=os.getcwd)
if os.path.isfile(os.path.join(path, "AB_MP2", filename)):
abfile = os.path.join(path, "AB_MP2", filename)
abfol = os.path.join(path, "AB_MP2")
elif os.path.isfile(os.path.join(path, "AB_HF", filename)):
abfile = os.path.join(path, "AB_HF", filename)
abfol = os.path.join(path, "AB_HF")
else:
abfile = False
json_filepath = jsonfile if ut.split_path(jsonfile)[0] else os.path.join(path, jsonfile)
old = ut.load_js(json_filepath) if os.path.isfile(json_filepath) else {}
new = {}
if abfile:
if not os.path.isfile(os.path.join(abfol, ccpfile)):
find_and_parse(abfol)
raw = ut.load_js(os.path.join(abfol, ccpfile))
coords = raw["frag_xyz"][-1][0]
if type(coords) == str:
coords = ut.vals_from_npz(os.path.join(abfol, coords), "frag_xyz")[-1][0].tolist()
elconf, cnt = [], 0
while not elconf: # if empty because "read", get previous
elconf = raw["elconf"][-1 - cnt][0]
cnt += 1
elconf = elconf[0] if len(elconf) == 1 else elconf[1]
bas = find_basfile(abfol)
new[prop_key] = [elconf, abfile, coords, bas]
if jsonfile:
old.update(new)
ut.dump_js(old, json_filepath)
return new
def get_all(fname, filename="Densmat_SCF.txt", ref="HF_ref", iso="HF_iso", FDET="HF_FDET",
jsonfile="DMfinder.json", ccpfile="CCParser.json"):
path = ut.split_path(fname)[0]
json_filepath = jsonfile if ut.split_path(jsonfile)[0] else os.path.join(path, jsonfile)
old = ut.load_js(json_filepath) if os.path.isfile(json_filepath) else {}
old.update(find_fdet_dmfiles(fname, filename=filename, prop_key=FDET,
jsonfile="", ccpfile=ccpfile)) # jsonfile="" because we only write at the end
old.update(find_ref_dmfile(fname, filename=filename, prop_key=ref,
jsonfile="", ccpfile=ccpfile))
old.update(find_iso_dmfiles(fname, filename=filename, prop_key=iso,
jsonfile="", ccpfile=ccpfile))
ut.dump_js(old, json_filepath)
def find_matrix(fname, wildcardlist=[], jsonfile="CCParser.json", prop_key="ext_DM"):
"""
"""
path = ut.split_path(fname)[0]
if not wildcardlist:
wildcardlist = ["Densmat_SCF.txt","Densmat_MP"] # TODO add other options
elif type(wildcardlist) not in [tuple, list]:
wildcardlist = [wildcardlist]
json_filepath = jsonfile if ut.split_path(jsonfile)[0] else os.path.join(path, jsonfile)
old = ut.load_js(json_filepath) if os.path.isfile(json_filepath) else {}
matching = [ut.split_path(fp)[1] for wc in wildcardlist for fp in gl.glob(os.path.join(path,wc))]
old[prop_key] = matching # always overwrites values because if file is no longer there, pointer is useless
ut.dump_js(old, json_filepath)
return matching
def locate_iso_dmfiles(path=None, filename="Densmat_SCF.txt", expansion="ME",
prop_key="HF_iso_{}", jsonfile="DMfinder.json",
ccpfile="CCParser.json"):
"""
"""
path = ut.deal_with_type(path, condition=None, to=os.getcwd)
if expansion == "ME":
if os.path.isfile(os.path.join(path, "A_MP2", filename)):
afile = os.path.join(path, "A_MP2", filename)
afol = os.path.join(path, "A_MP2")
elif os.path.isfile(os.path.join(path, "A_HF", filename)):
afile = os.path.join(path, "A_HF", filename)
afol = os.path.join(path, "A_HF")
else:
afile = False
if os.path.isfile(os.path.join(path, "B_MP2", filename)):
bfile = os.path.join(path, "B_MP2", filename)
bfol = os.path.join(path, "B_MP2")
elif os.path.isfile(os.path.join(path, "B_HF", filename)):
bfile = os.path.join(path, "B_HF", filename)
bfol = os.path.join(path, "B_HF")
else:
bfile = False
elif expansion == "SE":
if os.path.isfile(os.path.join(path, "A_MP2_gh", filename)):
afile = os.path.join(path, "A_MP2_gh", filename)
afol = os.path.join(path, "A_MP2_gh")
elif os.path.isfile(os.path.join(path, "A_HF", filename)):
afile = os.path.join(path, "A_HF_gh", filename)
afol = os.path.join(path, "A_HF_gh")
else:
afile = False
if os.path.isfile(os.path.join(path, "B_MP2_gh", filename)):
bfile = os.path.join(path, "B_MP2_gh", filename)
bfol = os.path.join(path, "B_MP2_gh")
elif os.path.isfile(os.path.join(path, "B_HF_gh", filename)):
bfile = os.path.join(path, "B_HF_gh", filename)
bfol = os.path.join(path, "B_HF_gh")
else:
bfile = False
else:
raise NotImplementedError("Unknown expansion!! Only ME and SE so far!")
json_filepath = jsonfile if ut.split_path(jsonfile)[0] else os.path.join(path, jsonfile)
old = ut.load_js(json_filepath) if os.path.isfile(json_filepath) else {}
new = {}
# if "{}" in prop_key:
# prop_key = prop_key.format(expansion)
if afile:
if not os.path.isfile(os.path.join(afol, ccpfile)):
find_and_parse(afol)
raw = ut.load_js(os.path.join(afol, ccpfile))
coords = raw["frag_xyz"][-1][0]
if type(coords) == str:
coords = ut.vals_from_npz(os.path.join(afol, coords), "frag_xyz")[-1][0].tolist()
coords = [[i[0].replace("@", "X-")]+i[1:] for i in coords]
elconf, cnt = [], 0
while not elconf: # if empty because "read", get previous
elconf = raw["elconf"][-1 - cnt][0]
cnt += 1
elconf = elconf[0] if len(elconf) == 1 else elconf[1]
basA = find_basfile(afol)
new[prop_key+"_A"] = [elconf, afile, coords, basA]
if bfile:
if not os.path.isfile(os.path.join(bfol, ccpfile)):
find_and_parse(afol)
raw = ut.load_js(os.path.join(bfol, ccpfile))
coords = raw["frag_xyz"][-1][0]
if type(coords) == str:
coords = ut.vals_from_npz(os.path.join(bfol, coords), "frag_xyz")[-1][0].tolist()
coords = [[i[0].replace("@", "X-")]+i[1:] for i in coords]
elconf, cnt = [], 0
while not elconf: # if empty because "read", get previous
elconf = raw["elconf"][-1 - cnt][0]
cnt += 1
elconf = elconf[0] if len(elconf) == 1 else elconf[1]
basB = find_basfile(bfol)
new[prop_key+"_B"] = [elconf, bfile, coords, basB]
if (afile or bfile) and jsonfile:
old.update(new)
ut.dump_js(old, json_filepath)
return new
def find_fdet_dmfiles(fname, filename="Densmat_SCF.txt", prop_key="HF_FDET",
jsonfile="DMfinder.json", ccpfile="CCParser.json"):
"""
"""
path = ut.split_path(fname)[0]
expansion = deduce_expansion(path=path)
afol, bfol = find_emb_A(path=path), find_emb_B(path=path)
if os.path.isfile(os.path.join(afol, filename)):
afile = os.path.join(afol, filename)
else:
afile = False
if os.path.isfile(os.path.join(bfol, filename)):
bfile = os.path.join(bfol, filename)
else:
bfile = False
json_filepath = jsonfile if ut.split_path(jsonfile)[0] else os.path.join(path, jsonfile)
old = ut.load_js(json_filepath) if os.path.isfile(json_filepath) else {}
new = {}
if afile:
if not os.path.isfile(os.path.join(afol, ccpfile)):
find_and_parse(afol)
raw = ut.load_js(os.path.join(afol, ccpfile))
coords = raw["frag_xyz"][-1][0]
if type(coords) == str:
npz = os.path.join(afol, coords)
coords = ut.vals_from_npz(npz, "frag_xyz")[-1][0].tolist()
if expansion == "SE":
ghost = ut.vals_from_npz(npz, "frag_xyz")[-1][1]
ghost[:,0] = "X-" + ghost[:,0]
coords.extend(ghost.tolist())
elif expansion == "SE":
ghost = raw["frag_xyz"][-1][1]
coords.extend([["X-"+i[0]]+i[1:] for i in ghost])
elconf, cnt = [], 0
while not elconf: # if empty because "read", get previous
elconf = raw["elconf"][-1 - cnt][0]
cnt += 1
elconf = elconf[0] if len(elconf) == 1 else elconf[1]
basA = find_basfile(afol)
new[prop_key+"_A"] = [elconf, afile, coords, basA]
if bfile:
if not os.path.isfile(os.path.join(bfol, ccpfile)):
find_and_parse(afol)
raw = ut.load_js(os.path.join(bfol, ccpfile))
coords, cnt = "read", 0
while coords == "read": # if empty because "read", get previous
coords = raw["frag_xyz"][-1 - cnt][0]
cnt += 1
if type(coords) == str:
npz = os.path.join(bfol, coords)
coords, cnt = "read", 0
while coords == "read": # if empty because "read", get previous
coords = ut.vals_from_npz(npz, "frag_xyz")[-1 - cnt][0].tolist()
cnt += 1
if expansion == "SE":
frag_xyz = ut.vals_from_npz(npz, "frag_xyz")
if frag_xyz.shape[1] == 1: # single fragment! probably B_gh
frag_xyz = frag_xyz[0, 0]
v_repl = np.vectorize(lambda x: x.replace("@", "X-"))
frag_xyz[:,0] = v_repl(frag_xyz[:,0])
coords = frag_xyz.tolist()
else:
ghost = ut.vals_from_npz(npz, "frag_xyz")[-1][1]
ghost[:,0] = "X-" + ghost[:,0]
coords.extend(ghost.tolist())
elif expansion == "SE":
frag_xyz = raw["frag_xyz"][-1]
if len(frag_xyz[-1]) == 1:
frag_xyz = frag_xyz[0, 0]
coords = [[i[0].replace("@", "X-")]+i[1:] if "@" in i[0] else i for i in frag_xyz]
else:
ghost = raw["frag_xyz"][-1][1]
coords.extend([["X-"+i[0]]+i[1:] for i in ghost])
elconf, cnt = [], 0
while not elconf: # if empty because "read", get previous
elconf = raw["elconf"][-1 - cnt][0]
cnt += 1
elconf = elconf[0] if len(elconf) == 1 else elconf[1]
basB = find_basfile(bfol)
new[prop_key+"_B"] = [elconf, bfile, coords, basB]
if (afile or bfile) and jsonfile:
old.update(new)
ut.dump_js(old, json_filepath)
return new
def elst_int_sum_iso(file,
jsfile="CCParser.json",
with_ccp=True,
linenumbers=True):
mainfol = ut.split_path(file)[0] if ut.split_path(file)[0] else os.getcwd()
# Get potentials
if os.path.isfile(os.path.join(mainfol, "v_coul.txt")):
v_j_file = os.path.join(mainfol, "v_coul.txt")
expansion = False
elif os.path.isfile(os.path.join(mainfol, "v_coulomb_ME.txt")):
v_j_file = os.path.join(mainfol, "v_coulomb_ME.txt")
expansion = "ME"
elif os.path.isfile(os.path.join(mainfol, "v_coulomb_SE.txt")):
v_j_file = os.path.join(mainfol, "v_coulomb_SE.txt")
expansion = "SE"
else:
raise FileNotFoundError("Cannot find the Coulomb potential file")
v_j = np.loadtxt(v_j_file)
if os.path.isfile(os.path.join(mainfol, "v_nucA.txt")):
v_a = np.loadtxt(os.path.join(mainfol, "v_nucA.txt"))
elif os.path.isfile(os.path.join(mainfol, "v_nuc_1.txt")):
v_a = np.loadtxt(os.path.join(mainfol, "v_nuc_1.txt"))
else:
raise FileNotFoundError("Cannot find file for v_A")
if os.path.isfile(os.path.join(mainfol, "v_nucB.txt")):
v_b = np.loadtxt(os.path.join(mainfol, "v_nucB.txt"))
elif os.path.isfile(os.path.join(mainfol, "v_nuc_0.txt")):
v_b = np.loadtxt(os.path.join(mainfol, "v_nuc_0.txt"))
else:
raise FileNotFoundError("Cannot find file for v_B")
# Get expansion
jsdata = ut.load_js(os.path.join(mainfol, jsfile)) if os.path.isfile(
os.path.join(mainfol, jsfile)) else {}
if "fde_expansion" in jsdata.keys():
if expansion:
assert expansion == jsdata["fde_expansion"][0][0] or jsdata[
"fde_expansion"][0] # linenumber or not
else:
expansion = jsdata["fde_expansion"][0]
if type(expansion) == list:
if not linenumbers:
warnings.warn(
"get_elst_int_sum: You are adding values without \"linenumbers\"\
in a json file which has them. This can lead to issues in reading data.\
Consider passing \"linenumbers=True\", dummy linenumbers will be added"
)
expansion = expansion[0]
elif linenumbers:
warnings.warn(
"get_elst_int_sum: You are adding values with \"linenumbers\"\
in a json file which does not have them. This can lead to issues in reading data.\
Consider passing \"linenumbers=False\"")
elif with_ccp:
import CCParser as ccp
parsed = ccp.Parser(file,
to_json=True,
json_file=jsfile,
to_console=False,
overwrite_file=False,
overwrite_vals=False)
# V_NN = parsed.results.V_AB.get_last() # check
if expansion:
assert expansion == parsed.results.fde_expansion[0]
else:
expansion = parsed.results.fde_expansion[0]
else:
try:
s = str(sp.check_output(
"grep -i expansion {}".format(file))).upper()
expansion = "ME" if "ME" in s else "SE"
except:
raise FileNotFoundError("Could not determine expansion")
# s = str(sp.check_output("grep \"Nuc_A <-> Nuc_B\" {}".format(file)))
# V_NN = float(re.search("-?\d+\.\d+",s).group())
#
# if "V_AB" in jsdata.keys:
# V_NN = jsdata["V_AB"][0]
# if type(V_NN) == list: # value and linenumber
# if not linenumbers:
# warnings.warn("get_elst_int_sum: You are adding values without \"linenumbers\"\
# in a json file which has them. This can lead to issues in reading data.\
# Consider passing \"linenumbers=True\", dummy linenumbers will be added")
# V_NN = V_NN[0]
# elif linenumbers:
# warnings.warn("get_elst_int_sum: You are adding values with \"linenumbers\"\
# in a json file which does not have them. This can lead to issues in reading data.\
# Consider passing \"linenumbers=False\"")
#
# Get DMs
if os.path.isfile(os.path.join(mainfol, "Densmat_A.txt")):
dmf_A = os.path.join(mainfol, "Densmat_A.txt")
elif os.path.isfile(
os.path.join(mainfol, "frag_1_HF_{}.txt".format(expansion))):
dmf_A = os.path.join(mainfol, "frag_1_HF_{}.txt".format(expansion))
if os.path.isfile(os.path.join(mainfol, "Densmat_B.txt")):
dmf_B = os.path.join(mainfol, "Densmat_B.txt")
elif os.path.isfile(
os.path.join(mainfol, "frag_0_HF_{}.txt".format(expansion))):
dmf_B = os.path.join(mainfol, "frag_0_HF_{}.txt".format(expansion))
dm_A = np.loadtxt(dmf_A,
dtype=np.float64,
skiprows=1 if has_header(file) else 0)
dm_B = np.loadtxt(dmf_B,
dtype=np.float64,
skiprows=1 if has_header(file) else 0)
lA, lB = dm_A.shape[0], dm_B.shape[0]
if is_square(lA):
nbasA = int(np.sqrt(lA))
dm_A = 2 * dm_A.reshape([nbasA, nbasA]) # NB supposes only alpha!!!
elif is_square(lA / 2):
nbasA = int(np.sqrt(lA / 2))
dm_A = dm_A.reshape([2, nbasA, nbasA]).sum(axis=0)
if is_square(lB):
nbasB = int(np.sqrt(lB))
dm_B = 2 * dm_B.reshape([nbasB, nbasB]) # NB supposes only alpha!!!
elif is_square(lB / 2):
nbasB = int(np.sqrt(lB / 2))
dm_B = dm_B.reshape([2, nbasB, nbasB]).sum(axis=0)
v_j = v_j.reshape([nbasA, nbasA])
v_b = v_b.reshape([nbasA, nbasA])
v_a = v_a.reshape([nbasB, nbasB])
J = np.einsum('ab,ba', v_j, dm_A)
AnucB = np.einsum('ab,ba', v_b, dm_A)
BnucA = np.einsum('ab,ba', v_a, dm_B)
if linenumbers:
J = [J, -1]
AnucB = [AnucB, -1]
BnucA = [BnucA, -1]
jsdata.update(
dict(J_sum_iso=[J], AnucB_sum_iso=[AnucB],
BnucA_sum_iso=[BnucA])) # Using same structure as ccp
ut.dump_js(jsdata, os.path.join(mainfol, jsfile))
def save_specs(self, fname):
specs = self.specs
ut.dump_js(specs, fname)