library_for_pin_depin

description:

• this is just a library for me to record the codes used to finish my Ph.D project.
• the repository has a series of workflows to operate HOOMD-blue;
• and has a library to proceed trajectories of particles in 2D and get their structural or kinetic properties

file structure:

• this library contains four parts: HOOMD-blue simulation module, data management module, data analysis module and application scripts.
• the filenames are listed as follows.
• HOOMD-blue simulation module: all files in symmetry_transformation.
• data management module: opertateOnMysql, proceed_file.
• data analysis module: points_analysis_2D, particle_tracking. particle_decorate data_decorate
• application scripts: list_code_analysis analysis_data_from_image workflow_part, workflow_analysis, data_analysis_cycle, getDataAndDiagram, and others.

get exp_data

• data_analysis_cycle.save_exp_20230113_6 #video_bond_traps
• workflow_analysis.show_bond_image
• particle_tracking.
• particle_decorate

log:

• 20240913 in workflow_analysis_achimedean.archimedean_tilings. add generate_cairo_part,generate_cairo edit generate_type_n,generate_type_n_part
• 20240419 in workflow_analysis_achimedean, edit generate_type_n_part, add generate_type5_part_center_fill, add generate_type6_part_superlattice_center_fill, add generate_type7_part_superlattice_center_fill, add generate_type9_part_superlattice_center_fill,
• 20240319 add plot_background in points_analysis_2D.bond_plot_module. edit save_feature in particle_tracking.particle_track add tune_pix2um, tune_um2pix in get_a_from_image.show_points_select
• 20240318 edit get_trap_positions in particle_tracking.save_points_from_exp add control_table_image_proceed edit restrict_axis_property_relative,plot_scale_bar in points_analysis_2D_freud.bond_plot_module_for_image
• 20240317 rename control_table_neighbor_change_evolution as control_table_string_like_motion add generate_type9_part_superlattice,generate_type9_superlattice in workflow_analysis.archimedean_tilings
• 20240308 add restrict in points_analysis_2D.dynamic_points_analysis_2d.plot_neighbor_change_evolution add show_pin_interstitial_order_parameter_v43 in workflow_analysis add plot_neighbor_change_evolution_finetune in points_analysis_2D.dynamic_points_analysis_2d add coarse_grainize_and_hist_average_data_log_with_dynamic_navg_odd in data_decorate.data_decorator.
• 20240306 edit plot_neighbor_change_evolution in points_analysis_2D.dynamic_points_analysis_2d
• 20240305 edit get_bonds_from_simu_indices_list_type_n in symmetry_transformation_v4_3.list_code_analysis.analyze_a_series_of_gsd_file add control_table_final_frame_bond add tune_dis in symmetry_transformation_v4_3.analysis_controller.get_bonds_png_from_a_gsd_frame
• 20240304 edit the order of fuctions in getDataAndDiagramCsv add get_diagram_binary_from_csv_type_n in getDataAndDiagramCsv add control_table_diagram edit *0.86466 from *0.99613 in get_cnks_from_csv_files_type_n_part.analyze_a_series_of_gsd_file. edit in list_code_analysis.analyze_a_series_of_gsd_file_dynamic.get_transformation_velocity_scan_csv_read
• 20240222 edit the position of get_cnks_from_csv_files_type_n_part in list_code_analysis.analyze_a_series_of_gsd_file edit get_transformation_velocity_scan_csv in list_code_analysis.analyze_a_series_of_gsd_file_dynamic
• 20240220 edit get_transformation_velocity_scan_csv in symmetry_transformation_v4_3.list_code_analysis.analyze_a_series_of_gsd_file_dynamic add stable in symmetry_transformation_v4_3.analysis_controller.get_data_from_a_trajectory add get_coordination_number_conditional(tune_dis) in symmetry_transformation_v4_3.analysis_controller.get_data_from_a_trajectory.get_cn_k_from_a_gsd_frame
• 20240219 edit get_saturate_time_of_tanh_like_data in points_analysis_2D.dynamic_points_analysis_2d. edit get_saturate_time_of_tanh_like_data in points_analysis_2D.dynamic_points_analysis_2d add data_analysis_cycle.save_from_txyz_to_cn3 edit count_coordination structure in points_analysis_2D.static_points_analysis_2d.get_coordination_number_conditional
• 20240218 add get_saturate_time_of_tanh_like_data in points_analysis_2D.dynamic_points_analysis_2d.
• 20240217 rename points_analysis_2D as points_analysis_2D_freud. move points_analysis_2D in lxt_code_py16_node to here. add ovariance_matrix_module in points_analysis_2D
• 20240126 edit init,get_cn_k_from_a_gsd_frame in symmetry_transformation_v4_3.analysis_controller.get_data_from_a_gsd_frame. add get_cnks_vs_t_from_csv in symmetry_transformation_v4_3.analysis_controller.analyze_a_series_of_gsd_file_dynamic add get_cnks in symmetry_transformation_v4_3.analysis_controller.get_data_from_a_trajectory add show_cn_k_logt in workflow_analysis.show_cn_k.
• 20240125 add get_radial_distribution_function in points_analysis_2D.static_points_analysis_2d from lxt_code_py16_node add get_trajectory_data_with_traps,get_trajectory_stable_data_with_traps in proceed_file.proceed_gsd_file to record triagnles, edit get_conditional_bonds_and_simplices_vertex_length in points_analysis_2D.static_points_analysis_2d
• 20240123 in workflow_analysis.archimedean_tilings. add generate_cairo_part,generate_cairo edit generate_type_n,generate_type_n_part edit init in workflow_analysis.archimedean_tilings_polygon_dye.
• 20240122 add merge_cnk_by_seed,merge_cnk_std_by_seed in getDataAndDiagramCsv
• 20240118 add check_PRE15 in function_plot.example_plot.functions_plot_module.
• 20240117 in symmetry_transformation_v4_3.list_code_analysis.analyze_a_series_of_gsd_file. edit get_cnks_from_csv_files_type_n_part upgrade gsd, hence .Snapshot->.Frame, .read_frame->._read_frame add generate_dipole,check_pre15 in function_plot.example_plot.functions_plot_module
• 20240116 in workflow_analysis.archimedean_tilings. add get_type_n_lcr0, get_coordination_number_k_for_type_n in symmetry_transformation_v4_3.list_code_analysis.analyze_a_series_of_gsd_file. edit get_cnks_from_csv_files_type_n_part
• 20240115 edit workflow_analysis.show_bond_image.read_image,draw_bond_exp_hex add points_analysis_2D.bond_plot_module.plot_scale_bar
• 20240111 add operate_simulation_langevin_wca_yukawa in simulation_core_p.simulation_core_traps add simulation_controller_wca_yukawa in simulation_controller_p add set_new_gsd_file in system_parameters_generators.initial_state_generator
• 20240105 add example_plot.generate_hertzian,generate_kob_andersen
• 20231227 add generate_simu_index_csv_depin_special_low_t in symmetry_transformation_v4_3.simulation_controller.simulation_controller_type_n_part_traps
• 20231226 add analysis_data_from_image, add_traps_to_points_kagome_part, draw_points_kagome_part, add_traps_to_points_honeycomb_part, draw_points_honeycomb_part
• 20231222 add get_cnks_from_csv_type_4569_part, get_cnks_from_csv_files_type_n_part in symmetry_transformation_v4_3.list_code_analysis.analyze_a_series_of_gsd_file
• 20231221 fix the problem of adding an unnamed column in symmetry_transformation_v4_3.list_code_analysis. analyze_a_series_of_gsd_fileget_cnks_from_csv_files_type_n
• 20231219 edit generate_initial_state_hex_particle_XXX_trap_scan_csv, col[i] -> 'col_name' to avoid new unnamed column:0.
• 20231217 add generate_initial_gsd_hex_and_type_n in symmetry_transformation_v4_3.simulation_controller
• 20231215 add get_cn5s_from_csv_files in symmetry_transformation_v4_3.list_code_analysis.analyze_a_series_of_gsd_file edit get_cn_k_from_a_gsd_frame in symmetry_transformation_v4_3.analysis_controller.get_data_from_a_gsd_frame
• 20231214 add generate_simu_index_csv_type_10_pin_3_30 in symmetry_transformation_v4_3.simulation_controller.simulation_controller_type_n_part_traps
• 20231213 add set_new_gsd_file_2types_by_box_or_n_size in symmetry_transformation_v4_3.system_parameters_generators.initial_state_generator edit generate_gaussian in function_plot.example_plot.functions_plot_module
• 20231212 add generate_initial_state_hexagonal_particle_honeycomb_part_gaus_eq_harmo_trap_scan_csv in symmetry_transformation_v4_3.simulation_controller add generate_gaussian_force, generate_harmonic_force, generate_gaussian, generate_harmonic in example_plot add get_bonds_from_simu_indices_type_n_from_csv in symmetry_transformation_v4_3.list_code_analysis.analyze_a_series_of_gsd_file
• 20231211 add get_2_k_cn3_stds_and_plot,get_cn3s_from_two_csv_files in symmetry_transformation_v4_3.list_code_analysis.analyze_a_series_of_gsd_file add merge_two_csvs in proceed_file. edit set_simulation_parameters self.width = 1 in simulation_core.simulation_core_traps
• 20231208 clear bond_plot_module_old in points_analysis_2D. add workflow_type_n in workflow_analysis.archimedean_tilings_polygon_dye. edit perturbation, fix positions.z = 0 in system_parameters_generators.initial_state_generator.set_new_gsd_file_2types_by_n_size
• 20231207 add generate_type_n_part,generate_type_n in workflow_analysis.archimedean_tilings
• 20231204 add trap_fill_box in system_parameters_generators.initial_state_generator.set_new_gsd_file_2types add get_gsds_from_mysql.get_record_from_csv
• 20231130 add get_conditional_bonds_and_simplices_bond_length in points_analysis_2D.static_points_analysis_2d. add workflow_analysis.archimedean_tilings_polygon_dye edit workflow_analysis.archimedean_tilings
• 20231127 add loadCsvDataToMysql, loadTxtDataToMysql in opertateOnMysql
• 20231124 add archimedean_tilings_polygon_dye in workflow_analysis. add generate_simu_index_csv in symmetry_transformation_v4_3.simulation_controller add generate_initial_state_hexagonal_particle_honeycomb_trap_scan_csv in symmetry_transformation_v4_3.simulation_controller
• 20231123 add cut_edge_of_positions_manual in points_analysis_2D.static_points_analysis_2d
• 20231122 edit simulation_controller.simulation_controller_traps.generate_initial_state_hexagonal_particle_honeycomb_trap add simulation_controller.simulation_controller_traps.generate_initial_state_hexagonal_particle_honeycomb_trap_scan_k
• 20231120 edit get_trajectory_data in proceed_file.proceed_gsd_file edit test_simulation
• 20231117 add generate_type10_part,generate_type10 in workflow_analysis.archimedean_tilings. add set_new_gsd_file_2types in system_parameters_generators.initial_state_generator.
• 20231116 add archimedean_tilings in workflow_analysis. add generate_type11_part,generate_type11 in workflow_analysis.archimedean_tilings.
• 20231115 add show_bonds_transition_from_hex_to_kagome in workflow_analysis. edit draw_points_with_given_bonds in points_analysis_2D.bond_plot_module for matplotlib update.
• 20231113 add symmetry_transformation_v4_3 to adjust the new hoomd.
• 20231107 add get_cn3_vs_u_sub_low_depin,txt_to_data_low_depin in workflow_analysis.controller_get_honey_cn3_vs_u_sub. add in workflow_analysis.controller_get_honey_part_cn3_vs_u_sub add saveIndexkTCN4CN3depin in data_analysis_cycle
• 20231106 add saveIndexkTCN4CN3SeedsPsi6 in data_analysis_cycle
• 20231027 add extend_traps_to_9boxes in workflow_analysis.workflow_temp
• 20231026 edit cut_edge_of_positions_by_box in points_analysis_2D.static_points_analysis_2d
• 20231025 add cut_edge_of_positions_by_box in points_analysis_2D.static_points_analysis_2d
• 20231019 add search_and_get_trajectory, search_and_get_single_final_frame in workflow_analysis.workflow_file_to_result. get_bond_trap_plot_param_compare
• 20231017 edit compute_energy_particle_wise in points_analysis_2D.energy_computer.
• 20231016 decouple get_extended_positions_from_points and get_extended_positions in proceed_file.proceed_gsd_file add compute_energy_particle_wise. in .
• 20231014 add interact_mode in points_analysis_2D.energy_computer.compute_distance
• 20231013 edit read_a_frame, adding dimension, in proceed_file.proceed_gsd_file. add get_extended_positions in proceed_file.proceed_gsd_file
• 20231012 edit the introduction of workflow_analysis. add data_retriever. add energy_computer to calculate the free energy of a system in in points_analysis_2d.
• 20231010 add array_to_xyz in proceed_file.data_type_transformer.
• 20230907 add plot_to_check_trans_ratio,plot_to_check_act_ratio,plot_to_check_act_share_ratio in workflow_analysis.show_pin_interstitial_order_parameter. add get_pin_depin_event in points_analysis_2d.dynamical_facilitation_module
• 20230906 add show_pin_interstitial_order_parameter in workflow_analysis add data_decorate add data_decorator in data_decorate add coarse_grainize_data_log,coarse_grainize_and_average_data_log in data_decorate.data_decorator
• 20230905 add get_interstitial_bool in points_analysis_2d.dynamical_facilitation_module
• 20230826 edit example in workflow_part.workflow_simu_to_mysql_pin_hex_to_kagome_oop_klt_2m add particle_decorate.py
• 20230814 edit workflow_part.workflow_simu_to_mysql_pin_hex_to_kagome_oop_klt_2m edit control_table
• 20230807 edit get_cost_function_cluster_ml
• 20230806 edit get_cost_function_cluster_ml
• 20230804 add polygon_analyzer_ml to reorganize get_conditional_bonds_and_simplices_ml and get_cost_function_cluster_ml add init() to relink vertices of rational ridge length in points_analysis_2d.static_points_analysis_2d.polygon_analyzer_ml edit two modes in points_analysis_2d.static_points_analysis_2d.polygon_analyzer_ml.get_conditional_bonds_and_simplices_ml
• 20230803 edit get_cost_function_cluster_ml
• 20230731 edit record_vertices_cluster[vertex_id, cluster_id], not initialize cluster_id as -1 but range(n_vertices) in points_analysis_2d.static_points_analysis_2d.get_conditional_bonds_and_simplices_ml. caution: edges not cut ! [x] in points_analysis_2d.static_points_analysis_2d.get_cost_function_cluster_ml. codes are finished but not checked [x]
• 20230730 edit get_conditional_bonds_and_simplices_ml in points_analysis_2d.static_points_analysis_2d[on going]
• 20230729 add account, filename_seed in data_analysis_cycle.saveIndexCN346PCairoSeed add account in workflow_part.workflow_simu_to_mysql_pin_hex_to_cairo_egct_uniform add get_conditional_bonds_and_simplices_ml in points_analysis_2d.static_points_analysis_2d add get_cost_function_cluster_ml in points_analysis_2d.static_points_analysis_2d
• 20230728 edit steps set option in pin_seed_oop.workflow_uniform.init(). edit pcairo1 in data_analysis_cycle.saveIndexCN346PCairoSeed solve passing over month bug in computeTime.getTimeCost
• 20230727 add example for get_trajectory_data in proceed_file.proceed_gsd_file rename function __init_state_launch as __launch_init_state in pin_seed_oop.
• 20230726 edit str_index=str(int(simu_index)) in data_analysis_cycle.save_from_gsd edit get_trajectory_data, add simu_index1 in proceed_file.proceed_gsd_file edit scp = pa.show_cairo_order_parameter(), overplot 'r+' in data_analysis_cycle.save_from_gsd(if p_cairo)
• 20230725 add introduction for compute_cairo_order_parameter in workflow_analysis.show_cairo_order_parameter. add get_cairo_order_parameter in points_analysis_2d.static_points_analysis_2d. link to show_cairo_order_parameter. move and edit show_cairo_order_parameter from workflow_analysis to points_analysis_2d.
• 20230724 add plot_bond_ridge_rank_idea in points_analysis_2d.static_points_analysis_2d, which is an idea of bond plot, bond_length_rank vs ridge_length_rank. add get_bonds_with_machine_learning_idea in points_analysis_2d.bond_plot_module [ongoing]
• 20230713 edit trajectory_coarse_grain_general in points_analysis_2d.trajectory_module add plot_bicolor_final_displacements_static in points_analysis_2d.trajectory_module add bond_plot_for_ai, particle large, trap small[ongoing] edit bond_plot_module.draw_points_with_given_bonds,plot_traps, draw_points_with_given_bonds in points_analysis_2d.
• 20230712 edit workflow_simu_to_mysql_pin_hex_to_kagome_oop_klt_2m precise in workflow_part scatt.workflow_mysql_to_data_pin_hex_to_kagome_klt_2m('remote')
• 20230711 edit plot_h_hp_cn3_scan_k_fast, add shallow honeycomb pin filename, in workflow_analysis.compare_diagram_dynamics add save_cn3_decorate_to_csv, save_cn3_decorate_to_csv_unit in workflow_analysis.compare_diagram_dynamics edit workflow_data_to_diagram_kagome_mark pin_check_s in getDataAndDiagram
• 20230710 add data_type_transformer.array_to_csv in proceed_file. edit save_from_gsd_to_cn3 in data_analysis_cycle edit record_lk36shallow = in getDataAndDiagram
• 20230707 edit draw_polygon_patch_oop polygon_color in points_analysis_2d.static_points_analysis_2d. edit trajectory_coarse_grain_general color_pin,color_inte in points_analysis_2d.trajectory_module
• 20230706 edit points_analysis_2d.trajectory_module. plot_bicolor_final_displacements, tune color. edit data_analysis_cycle.saveIndexklTCN3CN4Seed prefix_gsd -> prefix edit workflow_part.workflow_simu_to_mysql_pin_hex_to_kagome_oop_klt_2m k1 stp kend
• 20230703 edit save_from_gsd.bond_plot.draw_bonds_conditional_bond as draw_bonds_conditional_bond_oop add show_final_frame.search_lcr_k in workflow_analysis[finish] edit workflow_part.workflow_simu_to_mysql_pin_hex_to_kagome_oop_klt_2m edit data_analysis_cycle.saveIndexklTCN3CN4Seed to redirect prefix_gsd.
• 20230701 add show_final_frame.search_lcr_k in workflow_analysis[ongoing]
• 20230619 diagram sseries finished. edit workflow_part.workflow_simu_to_mysql_pin_hex_to_kagome edit symmetry_transformation.symmetry_transformation_auto_kagome_pin edit saveIndexCN4CN6SeedPsi6
• 20230615 add get_diagram_data_mark_multi in getDataAndDiagram.mysql_data_processor add workflow_data_to_diagram_honeycomb_mark, workflow_mysql_to_data_depin_from_honeycomb_mark, workflow_mysql_to_data_pin_hex_to_honeycomb_klt_2m_random_mark in getDataAndDiagram add workflow_data_to_diagram_kagome_mark, workflow_mysql_to_data_depin_from_kagome1_mark, workflow_mysql_to_data_pin_hex_to_kagome_klt_2m_random_mark in getDataAndDiagram add workflow_data_to_diagram_kagome_part_mark, workflow_mysql_to_data_depin_from_kagome_part1_mark, workflow_mysql_to_data_pin_hex_to_kagome_part_klt_2m_random_mark in getDataAndDiagram
• 20230614 add draw_diagram_scatter_mark_multi in getDataAndDiagram.mysql_data_processor add workflow_data_to_diagram_honeycomb_part_mark, workflow_mysql_to_data_depin_from_honeycomb_part1_mark, workflow_mysql_to_data_pin_hex_to_honeycomb_part_klt_2m_random_mark in getDataAndDiagram
• 20230613 add workflow_mysql_to_data_pin_hex_to_honeycomb_part_klt_2m_random_mark in getDataAndDiagram
• 20230612 redirect log_prefix to 2T disk in symmetry_transformation.pin_seed_oop.
• 20230610 add showTables in opertateOnMysql
• 20230609 add select_content in opertateOnMysql.getDataFromMysql add workflow_mysql_to_data_pin_hex_to_honeycomb_klt_2m_random in getDataAndDiagram
• 20230605 add dis_edge_cut in static_points_analysis_2d.__cut_edge_of_positions add dis_edge_cut in data_analysis_cycle.saveIndexCN346PCairoSeed add createTableInMysql in opertateOnMysql
• 20230603 add plot_diagram_value in getDataAndScatter rename getDataAndScatter as getDataAndDiagram
• 20230602 add data_decorating in workflow_analysis.compare_diagram_dynamics.
• 20230526 edit plot_polygon_bond_xylim in workflow_analysis.show_polygon_dye rename show_tuned_image as show_bond_image
• 20230525 edit trajectory_coarse_grain_single_particle in workflow_analysis.show_waiting_time_interstitial_motion add trajectory_module in points_analysis_2d edit get_points_plot_loop in workflow_analysis.show_polygon_dye
• 20230523 add self.image in particle_tracking.particle_track.single_frame_particle_tracking add file_name parameters in workflow_analysis.draw_tuned_image add axis_limit in particle_tracking.particle_track.single_frame_particle_tracking
• 20230519 add "ridge_length_method" in points_analysis_2d.static_points_analysis_2d.get_coordination_number_conditional
• 20230517 add first_two_peak_group_method in points_analysis_2d.static_points_analysis_2d.get_first_minima_bond_length_distribution edit "global_compare_method" to fix bug in 4323_8_2000
• 20230517 add compare_diagram_dynamics.plot_h_hp_cn3_scan_k_fast add compare_diagram_dynamics.get_data_cn3_scan_k_fast
• 20230516 simu is forced to stop
• 20230515 add compare_diagram_dynamics.plot_cn3_scan_k_fast(rename as plot_hp_cn3_scan_k_fast) add compare_diagram_dynamics.plot_honey_cn3_scan_k
• 20230512 edit workflow_simu_to_mysql_pin_hex_to_honeycomb_oop_klt_2m, check mode.[v]
• 20230511 add compare_diagram_dynamics.plot_cn3_scan_lcr
• 20230510 add compare_diagram.
• 20230508 add workflow_analysis.compare_diagram edit test_cuda.comapre_speed_cpu_vs_gpu
• 20230504 add file_for_CUDA.test_cuda
• 20230424 edit workflow_analysis.show_disp_field.get_bicolor_disp.
• 20230423 add workflow_part.saveIndexCN346PCairoSeed.
• 20230422 add workflow_analysis.show_cairo_order_parameter.
• 20230420 add proceed_file to operate files and make directories.
• 20230420 fix get_conditional_bonds_and_simplices, return count_polygon_relative
• 20230410 edit get_conditional_bonds_and_simplices, return count_polygon_relative
• 20230408 edit bond_plot_module init(ax=none)
• 20230404 add points_analysis_2d.count_polygon_n
• 20230329 add workflow_analysis.show_waiting_time_interstitial_motion add points_analysis_2d.dynamical_facilitation_module.scan_displacement_t
• 20230328 add workflow_analysis.optimize_polyfit add workflow_analysis.show_waiting_time_brownian add workflow_analysis.show_waiting_time_dynamical_facilitation
• 20230324 add workflow_analysis.show_tuned_image to add line over image. add bond_plot_module_for_image in points_analysis_2d
• 20230320 add workflow_uniform_continue in symmetry_transformation.simple_simulation add workflow_analysis.get_msd_from_gsd() add workflow_analysis.get_displacement_field_normal()
• 20230314 add workflow_analysis to record codes.
• 20230306 plot scatter vacancy and occupation in dynamical_facilitation_module.plot_reference_occupation add dynamical_facilitation_module.plot_reference_positions_waiting_time_colored
• 20230225 set honeycomb3-8-12 as facilitation reference, part1 as traps.
• 20230223 add probability distribution of dynamical facilitation(ongoing) add get_displacement_1D_overlap in data_analysis_cycle add dynamical_facilitation_module in points_analysis_2d
• 20230222 add function_plot including example_plot and unit_transform
• 20230216 add workflow_mysql_to_data_pin_hex_to_honeycomb_part_klt_2m_random_oop add mysql_data_processor in getDataAndScatter add get_string_like_motion_rank in data_analysis_workflow, add plot_string_like_motion_rank in dynamic_points_analysis_2d add get_displacement_field_xy_rank in displacemnt_field_2D
• 20230206 seperate draw_bonds_conditional_bond() into two parts( listed as follows) in bond_plot_module in points_analysis_2D part1, restrict_axis_property() part2, draw_points_with_conditional_bond()
• 20230131 add workflow_liquid in workflow_part add init_cut in dynamic_points_analysis_2d.plot_bond_neighbor_change_oop add __init_state_pin_from_gsd etc in pin_seed_oop add lattice_constant in coordination_number module in save_from_gsd
• 20230129 edit example in workflow_mysql_to_data_pin_hex_to_honeycomb_part_klt_2m() pip install latex, code added in bond_plot_module in points_analysis_2D
• 20230119 edit workflow_part.workflow_simu_to_mysql_pin_hex_to_honeycomb_part_oop_klt_2m() edit particle_tracking
• 20230118 edit data_analysis_cycle.data_analysis_workflow.get_displacment_field() generalize displacment_field_2D.get_displacement_field_xy() to any two frames. add savetxt function in plot_hist_neighbor_change_event() in points_analysis_2D.dynamic_points_analysis_2d add check mode in workflow_part.workflow_simu_to_mysql_pin_hex_to_honeycomb_part_oop_klt_2m() add zorder to rank plot object in figure, in
• 20230116 edit data_analysis.txyz_to_bond_plot,bond_plot_module 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. edit getDataAndScatter.
• 20230106 edit dynamic_points_analysis_2d.compute_nearest_neighbor_displacements & dynamic_coordination_bond_plot, static_points_analysis_2d.get_first_minima_bond_length_distribution & draw_bonds_conditional_bond in points_analysis_2d_CUDA fix error: 'ndarray' object cannot be interpreted as an integer fix error: 'BlockManager' object has no attribute 'columns' the main time cost is save numerous images.
• 20230105 fix bug of saving txyz as txyz_stable into 'txyz_stable.npy' update get_displacement_field_xy.given txyz_stable, cut_edge is not necessary anymore. move displacement_field_xy from proceed_gsd_file to dynamic_points_analysis_2d in points_analysis_2d it seems that while-loop proceeding static_points_analysis_2d is too slow. Implicit conversion to a NumPy array is not allowed. Please use .get() to construct a NumPy array explicitly. https://cloud.tencent.com/developer/ask/sof/927734
• 20230104 reorganize structure of points_analysis_2D.dynamic_points_analysis_2d edit proceed_gsd_file, dynamic_points_analysis_2d in points_analysis_2D
• 20230103 add monitor_neighbor_change_event(), bond_plot(), hist_neighbor_change_event() in points_analysis_2D.dynamic_points_analysis_2d
• 20230102 add sum_id_neighbors in static_points_analysis_2d.get_nearest_neighbor_dispalcement(), to check if neighbors of a center particle have changed over time.
• 20230101 set new standard of getDataAndScatter
• 20221219 invert the pixel coordination from image y-axis to coordination y-axis in particle_tracking.folder_frames_particle_tracking test data_analysis_cycle.save_points_from_exp, right. test and correct points_analysis_2d.dynamic_points_analysis_2d.compute_msd_normal, compute_atmsd_scan_t, compute_atmsd_t_chips
• 20221216 add data_analysis_cycle.save_points_from_exp, waiting test.
• 20221215 add Lindemann msd in dynamic_points_analysis_2d. rename points_analysis_2D as dynamic_points_analysis_2d
• 20221213 add points_analysis_2D.msd.compute_nn_msd()
• 20221212 add introduction, mode='simu'or'exp', plot_msd,plot_trajectory, for points_analysis_2D.msd
• 20221209 edit points_analysis_2D.msd
• 20221208 add kagome/honeycomb pin precise/low T
• 20221203 add seed in points_analysis_2D.proceed_gsd_file add points_analysis_2D.msd ongoing
• 20221202 cut edge in workflow_part.workflow_simu_to_mysql_depin_from_kagome; cut edge in workflow_part.workflow_simu_to_mysql_depin_from_honeycomb_part, add RandomSeed in data_analysis_cycle.saveIndexPsi3Psi6; cut edge in melt_hex_from_honeycomb; add simple_simulation; edit account in points_analysis_2D;
• 20221130 add psik_plot in data_analysis_cycle.save_from_gsd; add psi6 in workflow_mysql_to_data_pin_hex_to_honeycomb_part_klt_2m; add condition="where kT = 1" in workflow_mysql_to_data_pin_hex_to_honeycomb_part_klt_2m(account='tplab')
• 20221129 point_analysis_2D mean repalced by median; symmetry_transformation/pin_seed_oop.py add mode=""
• 20221128 pin_seed_oop.py add self.mode
• 20221128 add file get_a_from_image