Skip to content

Commit f14ecb4

Browse files
anthonyyleeanthonyylee
committed
Pre-release v0.1 - Added moved files
1 parent 88b8f2a commit f14ecb4

File tree

93 files changed

+5095299
-0
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

93 files changed

+5095299
-0
lines changed

‎original_paper_fortran_code/LIF_CombinedCR_Sept21.f90‎

Lines changed: 1150 additions & 0 deletions
Large diffs are not rendered by default.

‎original_paper_fortran_code/LIF_CombinedSCR_Sept21.f90‎

Lines changed: 1083 additions & 0 deletions
Large diffs are not rendered by default.

‎original_paper_fortran_code/look_missing_files_CCR.py‎

Lines changed: 131 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,131 @@
1+
import os,sys
2+
from time import sleep
3+
import numpy as np
4+
5+
program=sys.argv[1]
6+
Fortran_program='/'+str(program)
7+
8+
program2=sys.argv[2]
9+
Fortran_program2='/'+str(program2)
10+
11+
jobIndex=0 # this will increase at every loop iteration to and generate many job names
12+
cwd = os.getcwd() # this gets the path for the current directory
13+
per_taks_job=1
14+
#A= np.round( np.logspace(np.log10(0.05),0,40) , 4)
15+
16+
A=np.asarray([1])
17+
fCR=np.linspace(1,24,24).astype(int)
18+
Ms=np.linspace(2,50,25).astype(int)
19+
nets=np.array([1,2,3])
20+
21+
k=-1
22+
lxpr=len(Ms)*len(nets)*len(fCR)
23+
xpr=np.zeros([5,lxpr])
24+
for M1 in (Ms):
25+
for n1 in(nets):
26+
for f1 in (fCR):
27+
k=k+1
28+
xpr[0,k]=f1 # fcr
29+
xpr[1,k]=1 # Astim
30+
xpr[2,k]=M1 #M_electrode
31+
xpr[3,k]=1000 # stim duration
32+
xpr[4,k]=n1 # net_index
33+
34+
35+
36+
lb1=930
37+
38+
39+
40+
jobIndex=0
41+
for i in range (0,lxpr):
42+
jobIndex+=1
43+
44+
fcr1=xpr[0,i]
45+
Astim1=xpr[1,i]
46+
Mel=xpr[2,i]
47+
stim_dur=xpr[3,i]
48+
nindx=xpr[4,i]
49+
50+
nam1='1_odpar_fCR_'+str(int(fcr1*10))+'_M_'+str(int(Mel))+'_Astim_'+str(int(Astim1*1000))+'_net_'+str(int(nindx))+'_dur'+str(int(stim_dur))+'.dat'
51+
file=cwd+'/CCR/'+nam1
52+
53+
if os.path.isfile(file):
54+
print ("File exist")
55+
else:
56+
jobIndex+=1
57+
jobName='CCR_mis_'+str(jobIndex)
58+
with open(jobName+'.sh', 'w') as file: # write whatever you want to the file
59+
file.write(str('#!/bin/bash'+'\n'))
60+
file.write(str('#'+'\n'))
61+
file.write( str('#SBATCH --job-name='+str( jobName )+'\n' ) )
62+
file.write( str('#SBATCH --mail-type=FAIL'+'\n' ) )
63+
file.write( str('#SBATCH --mail-user=khaledi@stanford.edu'+'\n' ) )
64+
file.write(str('#SBATCH --time=48:00:00'+'\n'))
65+
file.write(str('#SBATCH --ntasks=1'+'\n'))
66+
file.write(str('#SBATCH --cpus-per-task=1'+'\n'))
67+
file.write(str('#SBATCH --mem-per-cpu=4G'+'\n'))
68+
file.write(str('#SBATCH --array=1'+'\n'))
69+
70+
# if jobIndex <= lb1 :
71+
# file.write(str('#SBATCH -p normal'+'\n'))
72+
# if jobIndex > lb1 :
73+
# file.write(str('#SBATCH -p ptass'+'\n'))
74+
#file.write(str('#SBATCH -p ptass'+'\n'))
75+
file.write(str('#SBATCH -p normal'+'\n'))
76+
file.write(str('#'+'\n'))
77+
# file.write( str('PER_TASK='+str( per_taks_job )+'\n' ) )
78+
# file.write( str('START_NUM=$(( ($SLURM_ARRAY_TASK_ID - 1) * $PER_TASK + 1 ))'+'\n' ) )
79+
# file.write( str('END_NUM=$(( $SLURM_ARRAY_TASK_ID * $PER_TASK ))'+'\n' ) )
80+
81+
file.write('srun ifort -o '+jobName+'.o ' + '-fast -c '+str(str(cwd)+Fortran_program+' \n'))
82+
file.write('srun ifort -o ' +jobName+'.x '+str(str(cwd)+'/'+jobName+'.o '+' \n'))
83+
# file.write( str('for (( ff1=1; ff1<=24; ff1=ff1+1 )); do'+'\n' ) )
84+
file.write(' srun '+str(str(cwd)+'/'+jobName+'.x'+' '+str(fcr1)+' '+str(Astim1)+' '+str(Mel)+' '+str(stim_dur) +' '+str(nindx)+'\n'))
85+
# file.write( str('done'+'\n' ) )
86+
87+
print(jobName,Mel,nindx)
88+
os.system("sbatch "+jobName+'.sh') # this will submit the job
89+
90+
91+
file=cwd+'/SCCR/'+nam1
92+
93+
if os.path.isfile(file):
94+
print ("File exist")
95+
else:
96+
jobIndex+=1
97+
jobName='SCCR_mis_'+str(jobIndex)
98+
with open(jobName+'.sh', 'w') as file: # write whatever you want to the file
99+
file.write(str('#!/bin/bash'+'\n'))
100+
file.write(str('#'+'\n'))
101+
file.write( str('#SBATCH --job-name='+str( jobName )+'\n' ) )
102+
file.write( str('#SBATCH --mail-type=FAIL'+'\n' ) )
103+
file.write( str('#SBATCH --mail-user=khaledi@stanford.edu'+'\n' ) )
104+
file.write(str('#SBATCH --time=48:00:00'+'\n'))
105+
file.write(str('#SBATCH --ntasks=1'+'\n'))
106+
file.write(str('#SBATCH --cpus-per-task=1'+'\n'))
107+
file.write(str('#SBATCH --mem-per-cpu=4G'+'\n'))
108+
file.write(str('#SBATCH --array=1'+'\n'))
109+
110+
# if jobIndex <= lb1 :
111+
# file.write(str('#SBATCH -p normal'+'\n'))
112+
# if jobIndex > lb1 :
113+
# file.write(str('#SBATCH -p ptass'+'\n'))
114+
#file.write(str('#SBATCH -p ptass'+'\n'))
115+
file.write(str('#SBATCH -p normal'+'\n'))
116+
file.write(str('#'+'\n'))
117+
# file.write( str('PER_TASK='+str( per_taks_job )+'\n' ) )
118+
# file.write( str('START_NUM=$(( ($SLURM_ARRAY_TASK_ID - 1) * $PER_TASK + 1 ))'+'\n' ) )
119+
# file.write( str('END_NUM=$(( $SLURM_ARRAY_TASK_ID * $PER_TASK ))'+'\n' ) )
120+
121+
file.write('srun ifort -o '+jobName+'.o ' + '-fast -c '+str(str(cwd)+Fortran_program2+' \n'))
122+
file.write('srun ifort -o ' +jobName+'.x '+str(str(cwd)+'/'+jobName+'.o '+' \n'))
123+
# file.write( str('for (( ff1=1; ff1<=24; ff1=ff1+1 )); do'+'\n' ) )
124+
file.write(' srun '+str(str(cwd)+'/'+jobName+'.x'+' '+str(fcr1)+' '+str(Astim1)+' '+str(Mel)+' '+str(stim_dur) +' '+str(nindx)+'\n'))
125+
# file.write( str('done'+'\n' ) )
126+
127+
print(jobName,Mel,nindx,fcr1)
128+
os.system("sbatch "+jobName+'.sh') # this will submit the job
129+
130+
131+

‎original_paper_fortran_code/look_missing_files_CCR_RS.py‎

Lines changed: 131 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,131 @@
1+
import os,sys
2+
from time import sleep
3+
import numpy as np
4+
5+
program=sys.argv[1]
6+
Fortran_program='/'+str(program)
7+
8+
program2=sys.argv[2]
9+
Fortran_program2='/'+str(program2)
10+
11+
jobIndex=0 # this will increase at every loop iteration to and generate many job names
12+
cwd = os.getcwd() # this gets the path for the current directory
13+
per_taks_job=1
14+
#A= np.round( np.logspace(np.log10(0.05),0,40) , 4)
15+
16+
A=np.asarray([1])
17+
fCR=np.linspace(1,24,24).astype(int)
18+
Ms=np.linspace(2,50,25).astype(int)
19+
nets=np.array([1,2,3])
20+
21+
k=-1
22+
lxpr=len(Ms)*len(nets)*len(fCR)
23+
xpr=np.zeros([5,lxpr])
24+
for M1 in (Ms):
25+
for n1 in(nets):
26+
for f1 in (fCR):
27+
k=k+1
28+
xpr[0,k]=f1 # fcr
29+
xpr[1,k]=1 # Astim
30+
xpr[2,k]=M1 #M_electrode
31+
xpr[3,k]=1000 # stim duration
32+
xpr[4,k]=n1 # net_index
33+
34+
35+
36+
lb1=930
37+
38+
39+
40+
jobIndex=0
41+
for i in range (0,lxpr):
42+
jobIndex+=1
43+
44+
fcr1=xpr[0,i]
45+
Astim1=xpr[1,i]
46+
Mel=xpr[2,i]
47+
stim_dur=xpr[3,i]
48+
nindx=xpr[4,i]
49+
50+
nam1='1_odpar_fCR_'+str(int(fcr1*10))+'_M_'+str(int(Mel))+'_Astim_'+str(int(Astim1*1000))+'_net_'+str(int(nindx))+'_dur'+str(int(stim_dur))+'.dat'
51+
file=cwd+'/CCR_RS/'+nam1
52+
53+
if os.path.isfile(file):
54+
print ("File exist")
55+
else:
56+
jobIndex+=1
57+
jobName='CCR_mis_'+str(jobIndex)
58+
with open(jobName+'.sh', 'w') as file: # write whatever you want to the file
59+
file.write(str('#!/bin/bash'+'\n'))
60+
file.write(str('#'+'\n'))
61+
file.write( str('#SBATCH --job-name='+str( jobName )+'\n' ) )
62+
file.write( str('#SBATCH --mail-type=FAIL'+'\n' ) )
63+
file.write( str('#SBATCH --mail-user=khaledi@stanford.edu'+'\n' ) )
64+
file.write(str('#SBATCH --time=48:00:00'+'\n'))
65+
file.write(str('#SBATCH --ntasks=1'+'\n'))
66+
file.write(str('#SBATCH --cpus-per-task=1'+'\n'))
67+
file.write(str('#SBATCH --mem-per-cpu=4G'+'\n'))
68+
file.write(str('#SBATCH --array=1'+'\n'))
69+
70+
# if jobIndex <= lb1 :
71+
# file.write(str('#SBATCH -p normal'+'\n'))
72+
# if jobIndex > lb1 :
73+
# file.write(str('#SBATCH -p ptass'+'\n'))
74+
#file.write(str('#SBATCH -p ptass'+'\n'))
75+
file.write(str('#SBATCH -p normal'+'\n'))
76+
file.write(str('#'+'\n'))
77+
# file.write( str('PER_TASK='+str( per_taks_job )+'\n' ) )
78+
# file.write( str('START_NUM=$(( ($SLURM_ARRAY_TASK_ID - 1) * $PER_TASK + 1 ))'+'\n' ) )
79+
# file.write( str('END_NUM=$(( $SLURM_ARRAY_TASK_ID * $PER_TASK ))'+'\n' ) )
80+
81+
file.write('srun ifort -o '+jobName+'.o ' + '-fast -c '+str(str(cwd)+Fortran_program+' \n'))
82+
file.write('srun ifort -o ' +jobName+'.x '+str(str(cwd)+'/'+jobName+'.o '+' \n'))
83+
# file.write( str('for (( ff1=1; ff1<=24; ff1=ff1+1 )); do'+'\n' ) )
84+
file.write(' srun '+str(str(cwd)+'/'+jobName+'.x'+' '+str(fcr1)+' '+str(Astim1)+' '+str(Mel)+' '+str(stim_dur) +' '+str(nindx)+'\n'))
85+
# file.write( str('done'+'\n' ) )
86+
87+
print(jobName,Mel,nindx,fcr1)
88+
os.system("sbatch "+jobName+'.sh') # this will submit the job
89+
90+
91+
file=cwd+'/SCCR_RS/'+nam1
92+
93+
if os.path.isfile(file):
94+
print ("File exist")
95+
else:
96+
jobIndex+=1
97+
jobName='SCCR_mis_'+str(jobIndex)
98+
with open(jobName+'.sh', 'w') as file: # write whatever you want to the file
99+
file.write(str('#!/bin/bash'+'\n'))
100+
file.write(str('#'+'\n'))
101+
file.write( str('#SBATCH --job-name='+str( jobName )+'\n' ) )
102+
file.write( str('#SBATCH --mail-type=FAIL'+'\n' ) )
103+
file.write( str('#SBATCH --mail-user=khaledi@stanford.edu'+'\n' ) )
104+
file.write(str('#SBATCH --time=48:00:00'+'\n'))
105+
file.write(str('#SBATCH --ntasks=1'+'\n'))
106+
file.write(str('#SBATCH --cpus-per-task=1'+'\n'))
107+
file.write(str('#SBATCH --mem-per-cpu=4G'+'\n'))
108+
file.write(str('#SBATCH --array=1'+'\n'))
109+
110+
# if jobIndex <= lb1 :
111+
# file.write(str('#SBATCH -p normal'+'\n'))
112+
# if jobIndex > lb1 :
113+
# file.write(str('#SBATCH -p ptass'+'\n'))
114+
#file.write(str('#SBATCH -p ptass'+'\n'))
115+
file.write(str('#SBATCH -p normal'+'\n'))
116+
file.write(str('#'+'\n'))
117+
# file.write( str('PER_TASK='+str( per_taks_job )+'\n' ) )
118+
# file.write( str('START_NUM=$(( ($SLURM_ARRAY_TASK_ID - 1) * $PER_TASK + 1 ))'+'\n' ) )
119+
# file.write( str('END_NUM=$(( $SLURM_ARRAY_TASK_ID * $PER_TASK ))'+'\n' ) )
120+
121+
file.write('srun ifort -o '+jobName+'.o ' + '-fast -c '+str(str(cwd)+Fortran_program2+' \n'))
122+
file.write('srun ifort -o ' +jobName+'.x '+str(str(cwd)+'/'+jobName+'.o '+' \n'))
123+
# file.write( str('for (( ff1=1; ff1<=24; ff1=ff1+1 )); do'+'\n' ) )
124+
file.write(' srun '+str(str(cwd)+'/'+jobName+'.x'+' '+str(fcr1)+' '+str(Astim1)+' '+str(Mel)+' '+str(stim_dur) +' '+str(nindx)+'\n'))
125+
# file.write( str('done'+'\n' ) )
126+
127+
print(jobName,Mel,nindx,fcr1)
128+
os.system("sbatch "+jobName+'.sh') # this will submit the job
129+
130+
131+

‎original_paper_fortran_code/model_input.in‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
2.d-2 !lamda
2+
2500.d0 ! tmax in seconds
3+
10.d0 ! save data every 10 second
4+
400.d0 !capa max coupling
5+
1000 ! #neurons in a network 200, 500, or 1000,2000

‎original_paper_fortran_code/net_reg/1_N_1000_reg_N_window.net‎

Lines changed: 50 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,50 @@
1+
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
2+
21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
3+
41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
4+
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80
5+
81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
6+
101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
7+
121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140
8+
141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160
9+
161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
10+
181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200
11+
201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220
12+
221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240
13+
241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260
14+
261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280
15+
281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300
16+
301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320
17+
321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340
18+
341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360
19+
361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380
20+
381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400
21+
401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420
22+
421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440
23+
441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460
24+
461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480
25+
481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500
26+
501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520
27+
521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540
28+
541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560
29+
561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580
30+
581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600
31+
601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620
32+
621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640
33+
641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660
34+
661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680
35+
681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700
36+
701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720
37+
721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740
38+
741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760
39+
761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780
40+
781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800
41+
801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820
42+
821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840
43+
841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860
44+
861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880
45+
881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900
46+
901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920
47+
921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940
48+
941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960
49+
961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980
50+
981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000

0 commit comments

Comments
 (0)