Merge pull request #22 from XT-Lee/master6

cuda

README.md

@@ -5,6 +5,33 @@
 - and has a library to proceed trajectories of particles in 2D and get their structural or dynamic properties
 
 ## log:
+- 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, 

computeTime.py

@@ -33,4 +33,5 @@ def getTimeCost(t1,t2):
     else:
         print("start",t1.tm_hour,":",t1.tm_min,":",t1.tm_sec)
         print("end  ",t2.tm_hour,":",t2.tm_min,":",t2.tm_sec)
-        print("cost ",dt_h,":",dt_m,":",dt_s)
+        print("cost ",dt_h,":",dt_m,":",dt_s)
+

control_table.py

@@ -1,68 +1,20 @@
 #import threading
 import time
+import computeTime as ct
 tm1=time.localtime(time.time())
 
 
-R"""
-select * from pin_hex_to_honeycomb_part_klt_2m where HarmonicK = 700;
-| SimuIndex | HarmonicK | LinearCompressionRatio | kT   | Psi3     | Psi6     | RandomSeed |
-|      4302 |       700 |                   0.81 |    1 | 0.927068 | 0.123686 |          9 |
-
-select * from pin_hex_to_honeycomb_klt_2m where HarmonicK = 900;
-+-----------+-----------+------------------------+------+----------+----------+------------+
-| 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 |
-+-----------+-----------+------------------------+------+----------+----------+------------+
-"""
-#import getDataAndScatter as scatt
-#scatt.workflow_mysql_to_data_pin_hex_to_honeycomb_klt_2m(account='remote')
-
-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)
-"""
-import data_analysis_cycle as da
-import points_analysis_2D as pa
-import numpy as np
-path_to_results = '/home/remote/xiaotian_file/data/20221129/video_7'
-txyz_npy_filename = path_to_results+'/'+'txyz_stable.npy'
-txyz_stable = np.load(txyz_npy_filename)
-msds = pa.dynamic_points_analysis_2d(txyz_stable,mode='exp')
-msds.plot_trajectory_single_particle(path_to_results+'/traj_stable/')#trajectory_stable.png
-#txyz_stable[:] = txyz_stable[:]/2.0
-"""
-"""
-msds.compute_atmsd_t_chips(0.95)
-time_log_file = path_to_results+'/'+'DefaultVideo_7.txt'
-time_log = np.loadtxt(time_log_file)
-png_filename=path_to_results+'/'+'msd_scantchips_loglog_um_95%.png'
-msds.plot_msd(time_log,png_filename)
-"""
 
 
 
-
-
-"""
-ts_id_dxy['particle']
-#pa.compute_atmsd_t_chips(interval_max=0.9,msd_per_particle=True)
-path_to_folder = '/home/remote/xiaotian_file/data/20221129/video5/'
-time_log = path_to_folder+'DefaultVideo_5.txt'
-png_filename = path_to_folder+'particle_'+str(id)+'_'+'msds_loglog.png'
-pa.plot_msd_uniform(m_msd=1,time_log=time_log,png_filename=png_filename)
-"""
+import file_for_CUDA.test_cuda as tc
+tcc = tc.comapre_speed_cpu_vs_gpu()
+t1,t2,r2 = tcc.calculate_cpu(tcc.rm1)
+t1,t2,r2c = tcc.calculate_gpu(tcc.rm1)
 
 
 #time.sleep(1)
 tm2=time.localtime(time.time())
 #calculate the time cost
-import computeTime as ct
 ct.getTimeCost(tm1,tm2)
 

control_table2.py

@@ -0,0 +1,14 @@
+from sys import prefix
+import time
+tm1=time.localtime(time.time())
+
+import function_plot.example_plot as ep
+fpm = ep.functions_plot_module()
+
+#fpm.generate_compare()
+t,y = fpm.generate_glass_list()#(b=1,m=0.99)
+fpm.plot_function_glass(t,y)
+tm2=time.localtime(time.time())
+#calculate the time cost
+import computeTime as ct
+ct.getTimeCost(tm1,tm2)

data_analysis_cycle.py

@@ -2,6 +2,7 @@
 import numpy 
 import matplotlib.pyplot as plt
 import os
+import proceed_file as pf
 
 def saveIndexPsi3Psi6(start_index,end_index,k1,step,linear_compression_ratio):
     R"""
@@ -241,6 +242,51 @@ def saveIndexCN346Seed(start_index,end_index,k1,step,linear_compression_ratio,ra
 
 
 
+    save_file_name=prefix+str(start_index)+'-'+str(end_index)+'klcn346'
+    numpy.savetxt(save_file_name,record)
+    #print(record)
+    return save_file_name
+
+def saveIndexCN346PCairoSeed(start_index,end_index,k1,step,linear_compression_ratio,randomseed):
+    R"""
+    This function will save a txt file named 'start index - end index kl', which contains
+    n rows of data 
+    [ simu_index | HarmonicK | LinearCompressionRatio | 
+        CoordinationNum3Rate | CoordinationNum4Rate | 
+        CoordinationNum6Rate | PCairo | RandomSeed ]
+    """
+    diference_index=end_index-start_index+1
+    prefix='/home/tplab/Downloads/'
+    record=numpy.zeros((diference_index,8))
+
+    for index in numpy.linspace(start_index,end_index,diference_index):
+        data_filename=prefix+'index'+str(index.astype(int))
+        obj_of_simu_index = pa.static_points_analysis_2d(filename=data_filename)
+
+
+        record[(index-start_index).astype(int),0]=index
+
+        record[(index-start_index).astype(int),1]=k1+step*(index-start_index)
+
+        record[(index-start_index).astype(int),2]=linear_compression_ratio
+
+
+        obj_of_simu_index.get_coordination_number_conditional()
+        ccn=obj_of_simu_index.count_coordination_ratio
+        record[(index-start_index).astype(int),3]=ccn[3]
+
+        record[(index-start_index).astype(int),4]=ccn[4]
+
+        record[(index-start_index).astype(int),5]=ccn[6]
+
+        import workflow_analysis as wa
+        cp = wa.show_cairo_order_parameter()
+        record[(index-start_index).astype(int),6]=cp.compute_cairo_order_parameter(ccn[3],ccn[4])
+
+        record[(index-start_index).astype(int),7]=randomseed
+
+
+
     save_file_name=prefix+str(start_index)+'-'+str(end_index)+'klcn346'
     numpy.savetxt(save_file_name,record)
     #print(record)
@@ -730,7 +776,6 @@ def save_exp_20230113_6(i,stable=True):
     xy_adjust = center+trap_locate
     pos,trap_filename = spe.get_trap_positions(tsf_filename,xy_adjust,1,90)#
 
-    import points_analysis_2D as pa  
     directory = spe.path_to_results+'/'
     dataname = video_name
     if stable:
@@ -790,7 +835,7 @@ def save_exp_20230113_8(i,stable=True):
     xy_adjust = center+trap_locate
     pos,trap_filename = spe.get_trap_positions(tsf_filename,xy_adjust,1,90)#
 
-    import points_analysis_2D as pa  
+
     directory = spe.path_to_results+'/'
     dataname = video_name
     if stable:
@@ -1040,11 +1085,11 @@ def save_from_gsd(simu_index=None,seed=None,frame_cut=0,
     #load time steps
     if seed is None:
         str_index=str(int(simu_index))
-        gsd_data = pa.proceed_gsd_file(simu_index=simu_index)
+        gsd_data = pf.proceed_gsd_file(simu_index=simu_index)
     else:
         str_index=str(int(simu_index))+'_'+str(seed)
         file_gsd = log_prefix+'trajectory_auto'+str_index+'.gsd'#+'_'+str(seed)
-        gsd_data = pa.proceed_gsd_file(filename_gsd_seed=file_gsd,account=account)
+        gsd_data = pf.proceed_gsd_file(filename_gsd_seed=file_gsd,account=account)
 
     file_log=log_prefix+'log-output_auto'+str_index+'.log'#+'_'+str(seed)
     log_data = numpy.genfromtxt(fname=file_log, skip_header=True)
@@ -1308,6 +1353,8 @@ def save_from_gsd(simu_index=None,seed=None,frame_cut=0,
         plt.savefig(png_filename)
         plt.close()
     if coordination_number:
+        #txt_filename = prefix +'T_VS_CN_k_tcut'+'index'+str_index+'egcut'+'.txt'
+        #numpy.savetxt(txt_filename,record_cn)
         plt.figure()
         if frame_cut == 0:#frame_cut is set to abstract a part of the process to watch in detail
             #plt.plot(record_cn[:,0],record_cn[:,1],label='CN_0')
@@ -1510,6 +1557,7 @@ def get_bond_plot(self,directory,data_name=None,trap_filename=None,trap_lcr=None
             dpa.draw_bonds.plot_neighbor_change(txyz_stable,nb_change)
             dpa.draw_bonds.plot_traps(trap_filename,LinearCompressionRatio)
             """
+
     def get_defect_motion(self,directory,data_name=None,trap_filename=None,trap_lcr=None):
         file_txyz_stable = directory + 'txyz_stable.npy'
         txyz_stable = numpy.load(file_txyz_stable)
@@ -1599,8 +1647,85 @@ def get_a_frame(self,directory,frame_index):
         dpa = pa.dynamic_points_analysis_2d(txyz_stable,mode='simu')
         dpa.plot_a_frame_of_points(frame_index,directory+str(frame_index)+'.png')
 
+    def get_displacement_1D(self,directory,data_name=None):#,id=0
+        R"""
+        example:
+            import data_analysis_cycle as dac
+            daw = dac.data_analysis_workflow()
+            directory,data_name = daw.gsd_to_txyz(simu_index=4302,io_only=True)
+            daw.get_displacement_1D(directory,data_name)
+        """
+        file_txyz_stable = directory + 'txyz_stable.npy'
+        txyz_stable = numpy.load(file_txyz_stable)
+        sz = numpy.shape(txyz_stable)
+        #print(sz)
+        """
+        prefix = directory
+        folder_name = ''
+        isExists=os.path.exists(prefix+folder_name)
+        if not isExists:
+            os.makedirs(prefix+folder_name)
+            prefix = prefix+folder_name
+        """
+
+        #dpa = pa.dynamic_points_analysis_2d(txyz_stable,mode='simu')
+        #import points_analysis_2D as pa
+        #dp = pa.dynamic_points_analysis_2d(txyz_stable)
+        df = pa.dynamical_facilitation_module()
+        for id in range(sz[1]):
+            ax = df.plot_displacement_t(txyz_stable[:,id,:2])
+            png_filename = directory+data_name+'_'+str(int(id))+'.png'
+            ax.set_title(data_name+'_'+str(int(id)))
+            plt.savefig(png_filename)
+            plt.close()
+
+    def get_displacement_1D_overlap(self,directory,data_name=None):#,id=0
+        file_txyz_stable = directory + 'txyz_stable.npy'
+        txyz_stable = numpy.load(file_txyz_stable)
+        sz = numpy.shape(txyz_stable)
+        df = pa.dynamical_facilitation_module()
+        fig,ax = plt.subplots()
+        for id in range(sz[1]):#
+            df.plot_displacement_t(txyz_stable[:,id,:2],ax)
+        ax.set_xlabel('t (k steps)')
+        ax.set_ylabel('$\delta$r ($\sigma$)')
+        ax.set_title(data_name+'_'+str(int(id)))
+        png_filename = directory+data_name+'_dr_abs'+'.png'
+        plt.savefig(png_filename)
+        plt.close()
+
+    def scan_displacement_1D_overlap(self,directory,data_name=None):#,id=0
+        file_txyz_stable = directory + 'txyz_stable.npy'
+        txyz_stable = numpy.load(file_txyz_stable)
+        sz = numpy.shape(txyz_stable)
+        df = pa.dynamical_facilitation_module()
+        fig,ax = plt.subplots()
+        for id in range(sz[1]):#
+            df.plot_displacement_t(txyz_stable[:,id,:2],ax)
+            df.plot_scan_displacement_t(txyz_stable[:,id,:2],ax)
+        ax.set_xlabel('t (k steps)')
+        ax.set_ylabel('$\delta$r ($\sigma$)')
+        ax.set_title(data_name+'_'+str(int(id)))
+        png_filename = directory+data_name+'_dr_abs'+'.png'
+        plt.savefig(png_filename)
+        plt.close()
+
+    def get_displacement_1D_data(self,directory,data_name=None):
+        file_txyz_stable = directory + 'txyz_stable.npy'
+        txyz_stable = numpy.load(file_txyz_stable)
+        sz = numpy.shape(txyz_stable)
+        df = pa.dynamical_facilitation_module()
+
+        for id in range(sz[1]):#
+            df.plot_displacement_t(txyz_stable[:,id,:2])
+
+
 class transfer_txt_to_array:
     R"""
+    introduction:
+        to draw traps on bond_plot in exp, 
+        I have to transfer txt/tsf file into array
+
     example:
         import numpy as np
         import data_analysis_cycle as dac
@@ -1660,4 +1785,5 @@ def get_scatter(self,account,data):
         plt.colorbar()
         png_filename=prefix+'K_VS_T_Psi6_as_value'+postfix
         plt.savefig(png_filename)
-        plt.close()
+        plt.close()
+