def density():
# variables
density = dict()
# height
avg_gra_z1 = bt.atoms_average(
mybgf,
'atom.z',
selection="'C_2G' in atom.ffType and atom.rNo == 1")
avg_gra_z2 = bt.atoms_average(
mybgf,
'atom.z',
selection="'C_2G' in atom.ffType and atom.rNo == 2")
dist = avg_gra_z2 - avg_gra_z1
eff_dist = avg_gra_z2 - avg_gra_z1 - 2 * r_vdw_C
# volume
x = mytrj.pbc[t][0]
y = mytrj.pbc[t][1]
volume = x * y * dist
eff_volume = x * y * eff_dist
# density
density = mass / 6.022 / volume * 10
eff_density = mass / 6.022 / eff_volume * 10
return [
x, y, dist, mass, volume, eff_volume, eff_dist, density,
eff_density
]
def count_layer(bgf_file, trj_file, ff_file='', out_file=''):
'''counts number of O atoms in each layer.
'''
# variables
result = dict()
# 1. Load BGF
mybgf = bgf.BgfFile(bgf_file)
N_BGF_ATOMS = len(mybgf.a)
r_vdw_C = 3.38383824 / 2
# 2. Read LAMMPS Trajectory
mytrj = lt.lammpstrj(trj_file)
timesteps = mytrj.load()
N_ATOMS = mytrj.natoms[0]
if N_BGF_ATOMS != N_ATOMS:
nu.die(
"Number of atoms in trajectory file does not match with BGF file.")
# 4. Update coordinates from the snapshot
for t in tqdm.tqdm(timesteps,
ncols=120,
desc="Calculating graphene z positions"):
mybgf = get_timestep(mybgf, trj_file, t)
avg_gra_z1 = bt.atoms_average(
mybgf,
'atom.z',
selection="'C_2G' in atom.ffType and atom.rNo == 1")
avg_gra_z2 = bt.atoms_average(
mybgf,
'atom.z',
selection="'C_2G' in atom.ffType and atom.rNo == 2")
dist = avg_gra_z2 - avg_gra_z1
eff_dist = avg_gra_z2 - avg_gra_z1 - 2 * r_vdw_C
result[t] = [avg_gra_z1, avg_gra_z2, dist, eff_dist]
# 5. Analyze
timesteps = sorted(result.keys())
with open('z_position.test.dat', 'w') as f:
output = ''
for t in timesteps:
output += "%d " % t
output += "%8.3f %8.3f %8.3f %8.3f\n" % result[t]
f.write(output)
def calculate_sel_kwac(mybgf):
"""
Create a selection string by calculating some properties from mybgf to calculate hbonds of Kwac's structure
Input:
- bgf.BgfFile mybgf
Output:
- string sel
"""
type = "gra"
for atom in mybgf.a:
if "Mo" in atom.ffType:
type = "mos"
# find inwater boundary for selection
swr = 3.270615945 / 2
gwr = 3.057430885 / 2
margin = 5.0
gwa_y = bt.atoms_average(mybgf, 'atom.y', selection="'GWA' in atom.rName")
gwb_y = bt.atoms_average(mybgf, 'atom.y', selection="'GWB' in atom.rName")
if type == "gra":
avg_z1 = bt.atoms_average(
mybgf,
'atom.z',
selection="'C_R' in atom.ffType and 'GRA' in atom.rName"
) # gra bottom
avg_z2 = bt.atoms_average(
mybgf,
'atom.z',
selection="'C_R' in atom.ffType and 'GRB' in atom.rName"
) # gra top
actual_distance = avg_z2 - avg_z1
elif type == "mos":
avg_s3a_z2 = bt.atoms_average(
mybgf,
'atom.z',
selection="'S_3a' in atom.ffType and atom.rNo == 2") # mos2 top
avg_s3b_z1 = bt.atoms_average(
mybgf,
'atom.z',
selection="'S_3b' in atom.ffType and atom.rNo == 1") # mos2 bottom
actual_distance = avg_s3a_z2 - avg_s3b_z1
inwater_x = mybgf.CRYSTX[0]
inwater_y = gwb_y - gwa_y + 2 * gwr - 2 * margin
if type == "gra":
inwater_z = actual_distance - 2 * gwr
elif type == "mos":
inwater_z = actual_distance - 2 * swr
sel = "atom.y > {gwa_y} + {margin} and atom.y < {gwb_y} - {margin}".format(
**vars())
return sel
def main(bgf_filename, grps_filename, margin=0.0):
# initialization
grps_original_filename = grps_filename + ".original"
# keep original grps file at the first run
if not os.path.exists(grps_original_filename):
shutil.copy(grps_filename, grps_original_filename)
# read atoms from bgf file
mybgf = bgf.BgfFile(bgf_filename)
pbc = mybgf.CRYSTX[:3]
swr = 3.270615945 / 2 # (wwr + swr) / 2 (defined by eq. from Pradeep Kumar's 2005 PRL)
gwr = 3.057430885 / 2 # (wwr + cwr) / 2
# wrap water molecules
#mybgf = bt.periodicMoleculeSort(mybgf, pbc, selection="'WAT' in atom.rName", silent=False)
#mybgf.saveBGF(bgf_filename + '.wrap')
nu.warn("* Volume assignment from %s to %s" %
(bgf_filename, grps_filename))
'''
Overall structure of MoS2
-------------------------
-----------Gra
S_3b ----
Mo :rNo 2
S_3a ----
< layer_distance >
S_3b ----
Mo :rNo 1
S_3a ----
-----------Gra
'''
# configure regions
pbc_x = mybgf.CRYSTX[0]
pbc_y = mybgf.CRYSTX[1]
pbc_z = mybgf.CRYSTX[2]
# group 1: MoS2
avg_s3a_z1 = bt.atoms_average(
mybgf, 'atom.z',
selection="'S_3a' in atom.ffType and atom.rNo == 1") # mos2 bottom
avg_s3b_z1 = bt.atoms_average(
mybgf, 'atom.z',
selection="'S_3b' in atom.ffType and atom.rNo == 1") # mos2 bottom
avg_s3a_z2 = bt.atoms_average(
mybgf, 'atom.z',
selection="'S_3a' in atom.ffType and atom.rNo == 2") # mos2 top
avg_s3b_z2 = bt.atoms_average(
mybgf, 'atom.z',
selection="'S_3b' in atom.ffType and atom.rNo == 2") # mos2 top
mos2_x = pbc_x
mos2_y = pbc_y
mos2_z = avg_s3b_z1 - avg_s3a_z1 + 2 * swr
nu.warn("\t** MoS2 region **")
nu.warn("\t\t- Effective MoS2 region dimensions: %8.3f %8.3f %8.3f" %
(mos2_x, mos2_y, mos2_z))
# group 2: graphene walls
gwa_y = bt.atoms_average(mybgf, 'atom.y', selection="'GWA' in atom.rName")
gwb_y = bt.atoms_average(mybgf, 'atom.y', selection="'GWB' in atom.rName")
graphene_x = pbc_x
graphene_y = gwb_y - gwa_y + 2 * gwr
# group 3: inwater
actual_distance = avg_s3a_z2 - avg_s3b_z1
inwater_x = pbc_x
inwater_y = graphene_y - 2 * margin
inwater_z = actual_distance - 2 * swr # effective interlayer distance
graphene_z = pbc_z - mos2_z * 2 - inwater_z # graphene
nu.warn("\t** In-water region **")
nu.warn("\t\t- Actual interlayer distance: %8.3f" % actual_distance)
nu.warn("\t\t- Effective water region dimensions: %8.3f %8.3f %8.3f" %
(inwater_x, inwater_y, inwater_z))
# group 4: reservoir
outwater_x = pbc_x
outwater_y = pbc_y - graphene_y
outwater_z = pbc_z
nu.warn("\t** Reservoir water region **")
nu.warn("\t\t- dimensions: %8.3f %8.3f %8.3f" %
(outwater_x, outwater_y, outwater_z))
# find water locations
all_molecules = bt.getMoleculeList(mybgf)
all_ow = [
atom.aNo for atom in mybgf.a
if 'OW' in atom.ffType or 'HW' in atom.ffType
]
inwaters_ow = [
atom.aNo for atom in mybgf.a
if (atom.y > gwa_y + margin and atom.y < gwb_y -
margin and 'OW' in atom.ffType)
]
inwaters_ow_nomargin = [
atom.aNo for atom in mybgf.a
if (atom.y > gwa_y and atom.y < gwb_y and 'OW' in atom.ffType)
]
if margin:
nu.warn("\t- Margin specified: %8.3f" % margin)
diff = len(inwaters_ow_nomargin) - len(inwaters_ow)
if diff:
nu.warn(
"\t- About %s water molecules are discarded out of %s atoms located near the border."
% (diff, len(inwaters_ow_nomargin)))
# record inwater aNo
inwaters = []
for ano in inwaters_ow:
atom = mybgf.getAtom(ano)
inwaters.append(atom.aNo)
for i in atom.CONECT:
inwaters.append(i)
outwaters = [i for i in all_ow if not i in inwaters]
nu.warn("** Distinguishing water positions **")
nu.warn("\t- Found %d atoms in in-water region (%8.3f molecules)" %
(len(inwaters), (len(inwaters) / 3.0)))
nu.warn("\t- Found %d atoms in reservoir region (%8.3f molecules)" %
(len(outwaters), (len(outwaters) / 3.0)))
debug_selection = "same residue as (y > %8.3f and y < %8.3f and type OW)" % (
gwa_y, gwb_y)
nu.warn("VMD selection for inwaters: %s" % debug_selection)
# calculate volume
vol_mos2 = mos2_x * mos2_y * mos2_z
vol_graphene = graphene_x * graphene_y * graphene_z
vol_inwater = inwater_x * inwater_y * inwater_z
vol_outwater = outwater_x * outwater_y * outwater_z
# compute stats
nu.warn("** Stats for confined water **")
mass_inwater = 18.0154 * len(inwaters_ow)
density_inwater = mass_inwater / vol_inwater / 6.022 * 10
nu.warn("\t- Number: %d" % len(inwaters_ow))
nu.warn("\t- Density: %8.5f" % density_inwater)
# separate water group into inwater and outwater
nu.warn("\tModifying grps file %s.." % sys.argv[0])
g = grpfile(grps_original_filename)
if len(g.grp) == 3:
new_group_no = g.split_group(3, outwaters)
g.grp[1]['volume'] = vol_mos2
g.grp[2]['volume'] = vol_graphene
g.grp[3]['volume'] = vol_inwater
g.grp[4]['volume'] = vol_outwater
elif len(g.grp) == 2:
new_group_no = g.split_group(2, outwaters)
g.grp[1]['volume'] = vol_mos2 + vol_graphene
g.grp[2]['volume'] = vol_inwater
g.grp[3]['volume'] = vol_outwater
else:
nu.die("Error on group numbers on %s" % grps_original_filename)
#g.write(grps_filename, zip=False)
g.write(grps_filename, zip=True)
nu.warn("%s: Done." % sys.argv[0])
def main(bgf_filename, grps_filename, margin):
# initialization
grps_original_filename = grps_filename + ".original"
warn = ""
# keep original grps file at the first run
if not os.path.exists(grps_original_filename):
shutil.copy(grps_filename, grps_original_filename)
# read atoms from bgf file
mybgf = bgf.BgfFile(bgf_filename)
pbc = mybgf.CRYSTX[:3]
swr = 3.270615945 / 2 # (wwr + swr) / 2 (defined by eq. from Pradeep Kumar's 2005 PRL)
gwr = 3.057430885 / 2 # (wwr + cwr) / 2
# wrap water molecules
#mybgf = bt.periodicMoleculeSort(mybgf, pbc, selection="'WAT' in atom.rName", silent=False)
#mybgf.saveBGF(bgf_filename + '.wrap')
warn += "* Volume assignment from %s to %s" % (bgf_filename, grps_filename)
'''
Overall structure of MoS2
-------------------------
-----------Gra
S_3b ----
Mo :rNo 2
S_3a ----
< layer_distance >
S_3b ----
Mo :rNo 1
S_3a ----
-----------Gra
'''
# configure regions
pbc_x = mybgf.CRYSTX[0]
pbc_y = mybgf.CRYSTX[1]
pbc_z = mybgf.CRYSTX[2]
# group 1: MoS2
avg_s3a_z1 = bt.atoms_average(
mybgf, 'atom.z',
selection="'S_3a' in atom.ffType and atom.rNo == 1") # mos2 bottom
avg_s3b_z1 = bt.atoms_average(
mybgf, 'atom.z',
selection="'S_3b' in atom.ffType and atom.rNo == 1") # mos2 bottom
avg_s3a_z2 = bt.atoms_average(
mybgf, 'atom.z',
selection="'S_3a' in atom.ffType and atom.rNo == 2") # mos2 top
avg_s3b_z2 = bt.atoms_average(
mybgf, 'atom.z',
selection="'S_3b' in atom.ffType and atom.rNo == 2") # mos2 top
mos2_x = pbc_x
mos2_y = pbc_y
mos2_z = avg_s3b_z1 - avg_s3a_z1 + 2 * swr
warn += "\t** MoS2 region **"
warn += "\t\t- Effective MoS2 region dimensions: %8.3f %8.3f %8.3f" % (
mos2_x, mos2_y, mos2_z)
# group 2: graphene walls
gwa_y = bt.atoms_average(mybgf, 'atom.y', selection="'GWA' in atom.rName")
gwb_y = bt.atoms_average(mybgf, 'atom.y', selection="'GWB' in atom.rName")
graphene_x = pbc_x
graphene_y = gwb_y - gwa_y + 2 * gwr
# group 3: "real" inwater
actual_distance = avg_s3a_z2 - avg_s3b_z1
inwater_x = pbc_x
inwater_y = graphene_y - 2 * margin
inwater_z = actual_distance - 2 * swr # effective interlayer distance
graphene_z = pbc_z - mos2_z * 2 - inwater_z # graphene
warn += "\t** In-water region **"
warn += "\t\t- Actual interlayer distance: %8.3f" % actual_distance
warn += "\t\t- Effective water region dimensions: %8.3f %8.3f %8.3f" % (
inwater_x, inwater_y, inwater_z)
# group 4: marginal inwater
marginal_inwater_x = inwater_x
marginal_inwater_y = 2 * margin
marginal_inwater_z = inwater_z
# group 5: marginal reservoir
marginal_outwater_x = pbc_x
marginal_outwater_y = 2 * margin
marginal_outwater_z = pbc_z
# group 6: "real" reservoir
outwater_x = pbc_x
outwater_y = pbc_y - graphene_y - 2 * margin
outwater_z = pbc_z
warn += "\t** Reservoir water region **"
warn += "\t\t- dimensions: %8.3f %8.3f %8.3f" % (outwater_x, outwater_y,
outwater_z)
# find water locations
all_molecules = bt.getMoleculeList(mybgf)
all_ow = [
atom.aNo for atom in mybgf.a
if 'OW' in atom.ffType or 'HW' in atom.ffType
]
inwaters_ow = [
atom.aNo for atom in mybgf.a
if (atom.y > gwa_y + margin and atom.y < gwb_y -
margin and 'OW' in atom.ffType)
]
marginal_inwaters_ow = [
atom.aNo for atom in mybgf.a if
((atom.y > gwa_y and atom.y < gwa_y + margin) or
(atom.y > gwb_y - margin and atom.y < gwb_y)) and 'OW' in atom.ffType
] # marginal inwater
inwaters_ow_nomargin = [
atom.aNo for atom in mybgf.a
if (atom.y > gwa_y and atom.y < gwb_y and 'OW' in atom.ffType)
]
marginal_outwaters_ow = [
atom.aNo for atom in mybgf.a if
((atom.y > gwa_y - margin and atom.y < gwa_y) or
(atom.y > gwb_y and atom.y < gwb_y + margin)) and 'OW' in atom.ffType
] # marginal outwater
outwaters_ow = [
atom.aNo for atom in mybgf.a if not atom.aNo in inwaters_ow
and not atom.aNo in marginal_outwaters_ow
and not atom.aNo in marginal_inwaters_ow and 'OW' in atom.ffType
] # real outwater
print(
"inwaters_vmd: same residue as (y > {gwa_y} + {margin} and y < {gwb_y} - {margin} and type OW)"
.format(**vars()))
print(
"marginal_inwaters_vmd: same residue as (((y > {gwa_y} and y < {gwa_y} + {margin}) or (y > {gwb_y} - {margin} and y < {gwb_y})) and type OW)"
.format(**vars()))
print(
"inwaters_vmd_nomargin: same residue as (y > {gwa_y} and y < {gwb_y} and type OW)"
.format(**vars()))
print(
"marginal_outwaters_vmd: same residue as (((y > {gwa_y} - {margin} and y < {gwa_y}) or (y > {gwb_y} and y < {gwb_y} + {margin})) and type OW)"
.format(**vars()))
if len(inwaters_ow_nomargin
) != len(inwaters_ow) + len(marginal_inwaters_ow):
nu.warn(
"\t- About %s water molecules are discarded out of %s atoms located near the border."
% (diff, len(inwaters_ow_nomargin)))
warn += "\t- Margin specified: %8.3f\n" % margin
# record aNo
def get_atoms(lst):
result = []
for ano in lst:
atom = mybgf.getAtom(ano)
result.append(atom.aNo)
for i in atom.CONECT:
result.append(i)
return result
inwaters = get_atoms(inwaters_ow)
marginal_inwaters = get_atoms(marginal_inwaters_ow)
marginal_outwaters = get_atoms(marginal_outwaters_ow)
outwaters = get_atoms(outwaters_ow)
if not (len(inwaters) % 3 == 0 and len(marginal_inwaters) % 3 == 0
and len(marginal_outwaters) % 3 == 0 and len(outwaters) % 3 == 0):
warn += "----- Suspicious water molecules division found!!!! -----\n"
# calculate volume
vol_mos2 = mos2_x * mos2_y * mos2_z
vol_graphene = graphene_x * graphene_y * graphene_z
vol_inwater = inwater_x * inwater_y * inwater_z
vol_marginal_inwater = marginal_inwater_x * marginal_inwater_y * marginal_inwater_z
vol_outwater = outwater_x * outwater_y * outwater_z
vol_marginal_outwater = marginal_outwater_x * marginal_outwater_y * marginal_outwater_z
vol_total = pbc_x * pbc_y * pbc_z
vol_sum = vol_mos2 + vol_graphene + vol_inwater + vol_marginal_inwater + vol_outwater + vol_marginal_outwater
'''
# compute stats
nu.warn("** Stats for confined water **")
mass_inwater = 18.0154 * len(inwaters_ow)
density_inwater = mass_inwater / vol_inwater / 6.022 * 10
nu.warn("\t- Number: %d" % len(inwaters_ow))
nu.warn("\t- Density: %8.5f" % density_inwater)
'''
# compute stats
warn += "\n\n\t**** Stats for confined water ****\n"
warn += "\t- Number:\n"
warn += "\t\t real inwater / marginal inwater / marginal outwater / real outwater: %d %d %d %d\n" % (
len(inwaters_ow), len(marginal_inwaters_ow),
len(marginal_outwaters_ow), len(outwaters_ow))
warn += "\t\t (%5.1f %% %5.1f %% %5.1f %% %5.1f %%)\n" % (
float(len(inwaters_ow)) / len(all_ow) * 100,
float(len(marginal_inwaters_ow)) / len(all_ow) * 100,
float(len(marginal_outwaters_ow)) / len(all_ow) * 100,
float(len(outwaters_ow)) / len(all_ow) * 100)
warn += "\t- Volumes: \n"
warn += "\t\tvol_mos2: %.3f = %.3f * %.3f * %.3f\n" % (vol_mos2, mos2_x,
mos2_y, mos2_z)
warn += "\t\tvol_graphene: %.3f = %.3f * %.3f * %.3f\n" % (
vol_graphene, graphene_x, graphene_y, graphene_z)
warn += "\t\tvol_inwater: %.3f = %.3f * %.3f * %.3f\n" % (
vol_inwater, inwater_x, inwater_y, inwater_z)
warn += "\t\tvol_marginal_inwater: %.3f = %.3f * %.3f * %.3f\n" % (
vol_marginal_inwater, marginal_inwater_x, marginal_inwater_y,
marginal_inwater_z)
warn += "\t\tvol_marginal_outwater: %.3f = %.3f * %.3f * %.3f\n" % (
vol_marginal_outwater, marginal_outwater_x, marginal_outwater_y,
marginal_outwater_z)
warn += "\t\tvol_outwater: %.3f = %.3f * %.3f * %.3f\n" % (
vol_outwater, outwater_x, outwater_y, outwater_z)
if vol_sum != vol_total:
warn += "\n\t\t----- Suspicious volume division found!!!! Density might be different -----\n"
warn += "\t\tTotal volume: %8.3f, Sum of divisions: %8.3f\n" % (
vol_total, vol_sum)
warn += "\t- Density:\n"
density_inwater = 18.0154 * len(inwaters_ow) / vol_inwater / 6.022 * 10
density_marginal_inwater = 18.0154 * len(
marginal_inwaters_ow) / vol_marginal_inwater / 6.022 * 10
density_marginal_outwater = 18.0154 * len(
marginal_outwaters_ow) / vol_marginal_outwater / 6.022 * 10
density_outwater = 18.0154 * len(outwaters_ow) / vol_outwater / 6.022 * 10
warn += "\t\t real inwater / marginal inwater / marginal outwater / real outwater: %.3f %.3f %.3f %.3f\n" % (
density_inwater, density_marginal_inwater, density_marginal_outwater,
density_outwater)
# separate water group into inwater and outwater
warn += "\tModifying grps file %s.." % sys.argv[0]
g = grpfile(grps_original_filename)
#new_group_no = g.split_group(2, outwaters)
marginal_inwater_group_no = g.split_group(2, marginal_inwaters)
marginal_outwater_group_no = g.split_group(2, marginal_outwaters)
outwater_group_no = g.split_group(2, outwaters)
g.grp[1]['volume'] = vol_mos2 + vol_graphene
g.grp[2]['volume'] = vol_inwater
g.grp[marginal_inwater_group_no]['volume'] = vol_marginal_inwater
g.grp[marginal_outwater_group_no]['volume'] = vol_marginal_outwater
g.grp[outwater_group_no]['volume'] = vol_outwater
#g.write(grps_filename, zip=False)
g.write(grps_filename, zip=True)
warn += "%s: Done." % sys.argv[0]
print(
"Numbers: real inwater / marginal inwater / marginal outwater / real outwater: %d %d %d %d"
% (len(inwaters_ow), len(marginal_inwaters_ow),
len(marginal_outwaters_ow), len(outwaters_ow)))
print(
"Density: real inwater / marginal inwater / marginal outwater / real outwater: %.3f %.3f %.3f %.3f"
% (density_inwater, density_marginal_inwater,
density_marginal_outwater, density_outwater))
n = 0
for atom in mybgf.a:
if fftype in atom.ffType:
avg += atom.z
n += 1
return avg / float(n)
# residue name and residue number
for atom in moslayer.a:
atom.rName = "MOS"
atom.rNo = 1
# average z coord for Mo
avg_mo_z = bt.atoms_average(moslayer,
'atom.z',
selection="'Mo' in atom.ffType")
# assign ffType
for atom in tqdm.tqdm(moslayer.a, ncols=120, desc='Assigning ffTypes'):
if "S" in atom.ffType:
if atom.z > avg_mo_z:
atom.ffType = "S_3a"
else:
atom.ffType = "S_3b"
# remove infinite boundary
n_del = 0
for atom in tqdm.tqdm(moslayer.a, ncols=120, desc='Removing pbc bonds'):
a = [atom.x, atom.y, atom.z]
connected_ano = atom.CONECT
sys.exit(0)
print(sys.argv)
b = bgf.BgfFile(sys.argv[1])
if len(sys.argv) <= 3:
ff = os.environ['FF_CNT'].replace("'", "")
else:
ff = sys.argv[3]
mols = bgftools.getMoleculeList(b)
# GRA 1 : bottom sheet
# GRA 2 : top sheet
bottom = bt.atoms_average(
b, 'atom.z', selection="'S_3a' in atom.ffType and atom.rNo == 1") # bottom
top = bt.atoms_average(
b, 'atom.z', selection="'S_3b' in atom.ffType and atom.rNo == 2") # top
moved_atoms = ""
# round 3
for molecule in tqdm(mols):
if len(molecule) != 3:
continue
cx, cy, cz = bgftools.getCom(b, ff, aNo_list=molecule)
if abs(cz - top) < 0.5:
for ano in molecule:
atom = b.getAtom(ano)
if 'I' in atom.chain:
atom.z -= 2.0
out_file = sys.argv[2]
ff_file = sys.argv[3]
layer_dist = float(sys.argv[4])
n_wat = int(sys.argv[5])
margin = float(sys.argv[6])
gralayer = bgf.BgfFile(bgf_file)
# residue name and residue number
for atom in gralayer.a:
atom.rName = "GRA"
atom.rNo = 1
# average z coord for GRA
avg_gra_z = bt.atoms_average(gralayer,
'atom.z',
selection="'C_2G' in atom.ffType")
# copy
gralayer2 = copy.deepcopy(gralayer)
# move
for atom in tqdm.tqdm(gralayer2.a, ncols=120, desc='Translating'):
atom.rName = "GRA"
atom.rNo = 2
atom.z += layer_dist
# merge
result = gralayer.merge(gralayer2, True)
result.renumber()
'''
