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Merge pull request #20 from XT-Lee/master2
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edit bond_plot_oop
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@XT-Lee
XT-Lee authored Jan 16, 2023
2 parents 6926202 + cb2b8a0 commit 7dad27f
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4 changes: 4 additions & 0 deletions README.md
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Expand Up @@ -5,6 +5,10 @@
- and has a library to proceed trajectories of particles in 2D and get their structural or dynamic properties.

## log:
- 20230116 edit data_analysis.txyz_to_bond_plot,
dynamic_points_analysis_2d.plot_bond_neighbor_change_oop,
static_points_analysis_2d.draw_bonds_conditional_bond_oop,
create class bond_plot_module in points_analysis_2D
- 20230107 simplify pin_seed_oop
edit data_analysis_cycle.data_analysis
edit workflow_part.workflow_simu_to_mysql_pin_hex_to_honeycomb_oop_klt_2m.
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77 changes: 62 additions & 15 deletions data_analysis_cycle.py
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Expand Up @@ -1241,16 +1241,38 @@ class data_analysis:
+-----------+-----------+------------------------+------+----------+----------+------------+
| SimuIndex | HarmonicK | LinearCompressionRatio | kT | Psi3 | Psi6 | RandomSeed |
| 4634 | 900 | 0.79 | 1 | 0.862018 | 0.159095 | 9 |
select * from pin_hex_to_honeycomb_klt_2m where SimuIndex = 5238;
+-----------+-----------+------------------------+------+----------+----------+------------+
| SimuIndex | HarmonicK | LinearCompressionRatio | kT | Psi3 | Psi6 | RandomSeed |
+-----------+-----------+------------------------+------+----------+----------+------------+
| 5238 | 60 | 0.79 | 1 | 0.885731 | 0.196146 | 9 |
+-----------+-----------+------------------------+------+----------+----------+------------+
select * from pin_hex_to_kagome_part_klt_2m where CoordinationNum4Rate > 0.8;
+-----------+-----------+------------------------+------+----------------------+----------------------+------------+
| SimuIndex | HarmonicK | LinearCompressionRatio | kT | CoordinationNum3Rate | CoordinationNum4Rate | RandomSeed |
+-----------+-----------+------------------------+------+----------------------+----------------------+------------+
| 4428 | 300 | 0.87 | 1 | 0 | 0.821229 | 9 |
| 4435 | 1000 | 0.87 | 1 | 0.039548 | 0.824859 | 9 |
| 4439 | 400 | 0.88 | 1 | 0 | 0.852273 | 9 |
| 4440 | 500 | 0.88 | 1 | 0.0224719 | 0.848315 | 9 |
| 4445 | 1000 | 0.88 | 1 | 0.0168539 | 0.837079 | 9 |
| 4447 | 200 | 0.89 | 1 | 0.0449438 | 0.825843 | 9 |
| 4448 | 300 | 0.89 | 1 | 0.0167598 | 0.865922 | 9 |
| 4449 | 400 | 0.89 | 1 | 0.0224719 | 0.820225 | 9 |
| 4454 | 900 | 0.89 | 1 | 0.0225989 | 0.858757 | 9 |
+-----------+-----------+------------------------+------+----------------------+----------------------+------------+
"""
def __init__(self):
pass

def gsd_to_txyz(self,account='remote',simu_index=0,seed=9):
def gsd_to_txyz(self,account='remote',simu_index=0,seed=9,io_only=False):
R"""
input:
account: (string);
simu_index: (int)index;
seed: (int)0-9
io_only: just return results, not proceeding data.
return:
directory: (str)directory with '/';
data_name: (str)'index_seed' for example.
Expand All @@ -1264,22 +1286,31 @@ def gsd_to_txyz(self,account='remote',simu_index=0,seed=9):
os.makedirs(directory)

directory = directory+'/'
gsd = pa.proceed_gsd_file(account=account,simu_index=simu_index,seed=seed)
gsd.get_trajectory_data(directory)
gsd.get_trajectory_stable_data(directory)
if not io_only:
gsd = pa.proceed_gsd_file(account=account,simu_index=simu_index,seed=seed)
gsd.get_trajectory_data(directory)
gsd.get_trajectory_stable_data(directory)
return directory,str_simu_index

def txyz_to_bond_plot(self,directory,data_name=None):
def txyz_to_bond_plot(self,directory,data_name=None,trap_filename=None,trap_lcr=None,io_only=False):
R"""
input:
directory from self.gsd_to_txyz
trap_filename:
'/home/remote/hoomd-examples_0/testhoneycomb3-8-12'
'/home/remote/hoomd-examples_0/testhoneycomb3-8-12-part1'
'/home/remote/hoomd-examples_0/testkagome3-11-6'
'/home/remote/hoomd-examples_0/testkagome_part3-11-6'
io_only: just return results, not proceeding data.
return:
a series of figures with particles(mark neighbor changes), bonds, traps
example:
import data_analysis_cycle as da
get_traj = da.data_analysis()
directory,data_name = get_traj.gsd_to_txyz('remote',5238,9)
get_traj.txyz_to_bond_plot(directory,data_name)
directory,data_name = get_traj.gsd_to_txyz('remote',4448,9,io_only=True)
get_traj.txyz_to_bond_plot(directory,data_name,
trap_filename='/home/remote/hoomd-examples_0/testkagome_part3-11-6',trap_lcr=0.89,
io_only=True)
"""
#write a routine class
import pandas as pd
Expand All @@ -1288,17 +1319,33 @@ def txyz_to_bond_plot(self,directory,data_name=None):
dpa = pa.dynamic_points_analysis_2d(txyz_stable,mode='simu')
#particle id should be set as what in txyz_stable!
bond_cut_off = 6
#dpa.compute_nearest_neighbor_displacements(csv_prefix=directory,bond_cut_off=bond_cut_off)
file_ts_id_dxy = directory + 'ts_id_dxy.csv'
ts_id_dxy = pd.read_csv(file_ts_id_dxy)
dpa.monitor_neighbor_change_event(ts_id_dxy=ts_id_dxy,csv_prefix=directory)

if not io_only:
dpa.compute_nearest_neighbor_displacements(csv_prefix=directory,bond_cut_off=bond_cut_off)
file_ts_id_dxy = directory + 'ts_id_dxy.csv'
ts_id_dxy = pd.read_csv(file_ts_id_dxy)
if_nb_change_int,n_particle_nb_stable = dpa.monitor_neighbor_change_event(ts_id_dxy=ts_id_dxy,csv_prefix=directory)
dpa.plot_hist_neighbor_change_event(if_nb_change_int,n_particle_nb_stable,directory)
"""
if_nb_change_int, n_particle_nb_stable, png_filename==dpa.monitor_neighbor_change_event(ts_id_dxy=ts_id_dxy,csv_prefix=directory)
dpa.plot_hist_neighbor_change_event(if_nb_change_int, n_particle_nb_stable, png_filename=)
"""
if not data_name is None:
file_list_sum_id_nb_stable = directory + 'list_sum_id_nb_stable.csv'
list_sum_id_nb_stable = pd.read_csv(file_list_sum_id_nb_stable)
dpa.dynamic_coordination_bond_plot(nb_change=list_sum_id_nb_stable,data_name=data_name,prefix=directory,bond_cut_off=bond_cut_off,
show_traps=True,trap_filename='/home/remote/hoomd-examples_0/testhoneycomb3-8-12',trap_lcr=0.79)

#dpa.plot_bond_neighbor_change(nb_change=list_sum_id_nb_stable,data_name=data_name,prefix=directory,bond_cut_off=bond_cut_off,
# show_traps=True,trap_filename='/home/remote/hoomd-examples_0/testhoneycomb3-8-12',trap_lcr=0.79)
dpa.plot_bond_neighbor_change_oop(data_name=data_name,prefix=directory,nb_change=list_sum_id_nb_stable,bond_cut_off=bond_cut_off,
trap_filename=trap_filename,trap_lcr=trap_lcr)
"""
"""
"""
dpa.plot_bond_neighbor_change_oop()
dpa.draw_bonds.draw_bonds_conditional_bond()
dpa.draw_bonds.plot_neighbor_change(txyz_stable,nb_change)
dpa.draw_bonds.plot_traps(trap_filename,LinearCompressionRatio)
"""

def get_msd(self,pixel_to_um=3.0/32.0,um_to_sigma=1.0/2.0):
txyz_npy_filename = self.path_to_results+'/'+'txyz_stable'
traj = numpy.load(txyz_npy_filename)
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