repo stringlengths 1 99 | file stringlengths 13 215 | code stringlengths 12 59.2M | file_length int64 12 59.2M | avg_line_length float64 3.82 1.48M | max_line_length int64 12 2.51M | extension_type stringclasses 1
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tps-torch | tps-torch-main/dimer_solv/ml_test/nn_initialization.py | #import sys
#sys.path.insert(0,"/global/home/users/muhammad_hasyim/tps-torch/build")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from dimer_ftsus import FTSLayerUSCustom as FTSLayer
from committor_nn im... | 4,668 | 32.589928 | 181 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/plotmodel.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
#from brownian_ml import CommittorNet
from committor_nn import CommittorNet, CommittorNetBP, CommittorNetDR
import numpy as np
#Import... | 2,791 | 27.489796 | 112 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/dimer_us.py | import sys
sys.path.insert(0,'/global/home/users/muhammad_hasyim/tps-torch/build/')
#Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.examples.dimer_solv_ml import MyMLEXPSampler
from tpstorch import _rank, _wo... | 4,070 | 32.097561 | 107 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/run_us_sl.py | import sys
sys.path.append("..")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from dimer_us import DimerUS
from committor_nn import CommittorNetDR
from tpstorch.ml.data import EXPReweightSimulation
from ... | 5,785 | 32.062857 | 187 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/dimer_fts_nosolv.py | import sys
sys.path.insert(0,'/global/home/users/muhammad_hasyim/tps-torch/build/')
import scipy.spatial
#Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.examples.dimer_solv_ml import MyMLFTSSampler
from tpsto... | 9,628 | 36.034615 | 122 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/committor_nn.py | #Import necessarry tools from torch
import torch
import torch.nn as nn
import numpy as np
#Import any other thing
import tqdm, sys
# SchNet imports
from typing import Optional
import os
import warnings
import os.path as osp
from math import pi as PI
import torch.nn.functional as F
from torch.nn import Embedding, Se... | 15,044 | 34.736342 | 107 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/dimer_ftsus_nosolv.py | import sys
sys.path.insert(0,'/global/home/users/muhammad_hasyim/tps-torch/build/')
import scipy.spatial
#Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.examples.dimer_solv_ml import MyMLEXPStringSampler
from... | 12,403 | 38.129338 | 122 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/ftsme/run_ftsme_r.py | import sys
sys.path.append("..")
import time
t0 = time.time()
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
import scipy.spatial
#Import necessarry tools from tpstorch
from dimer_fts_nosolv import dimer_reorient, DimerFTS
from committor_nn imp... | 7,280 | 40.135593 | 181 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/ftsme/run_ftsme.py | import sys
sys.path.append("..")
import time
t0 = time.time()
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
import scipy.spatial
#Import necessarry tools from tpstorch
from dimer_fts_nosolv import dimer_reorient, DimerFTS
from committor_nn imp... | 6,468 | 43.308219 | 218 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/ftsus/run_ftsus.py | import sys
sys.path.append("..")
import time
t0 = time.time()
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
import scipy.spatial
#Import necessarry tools from tpstorch
from dimer_ftsus_nosolv import DimerFTSUS
from committor_nn import initiali... | 5,510 | 37.538462 | 210 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/ftsus/run_ftsus_r.py | import sys
sys.path.append("..")
import time
t0 = time.time()
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
import scipy.spatial
#Import necessarry tools from tpstorch
from dimer_ftsus_nosolv import DimerFTSUS
from committor_nn import initiali... | 5,652 | 37.455782 | 210 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/us/run_us_r.py | import sys
sys.path.append("..")
import time
t0 = time.time()
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from dimer_us import DimerUS
from committor_nn import initializeConfig, CommittorNet, CommittorN... | 5,262 | 33.625 | 181 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/us/run_us.py | import sys
sys.path.append("..")
import time
t0 = time.time()
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from dimer_us import DimerUS
from committor_nn import initializeConfig, CommittorNet, CommittorN... | 5,120 | 33.601351 | 181 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/ftsus_sl/run_ftsus_sl_r.py | import sys
sys.path.append("..")
import time
t0 = time.time()
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
import scipy.spatial
#Import necessarry tools from tpstorch
from dimer_ftsus_nosolv import DimerFTSUS
from committor_nn import initiali... | 7,980 | 37.742718 | 197 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/ftsus_sl/run_ftsus_sl.py | import sys
sys.path.append("..")
import time
t0 = time.time()
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
import scipy.spatial
#Import necessarry tools from tpstorch
from dimer_ftsus_nosolv import DimerFTSUS
from committor_nn import initiali... | 7,539 | 37.274112 | 197 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/ftsme_sl/run_ftsme_sl_r.py | import sys
sys.path.append("..")
import time
t0 = time.time()
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
import scipy.spatial
#Import necessarry tools from tpstorch
from dimer_fts_nosolv import dimer_reorient, DimerFTS
from committor_nn imp... | 9,196 | 40.995434 | 181 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/ftsme_sl/run_ftsme_sl.py | import sys
sys.path.append("..")
import time
t0 = time.time()
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
import scipy.spatial
#Import necessarry tools from tpstorch
from dimer_fts_nosolv import dimer_reorient, DimerFTS
from committor_nn imp... | 8,699 | 40.626794 | 181 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/ftme_sl/dimer_fts_nosolv.py | import sys
sys.path.insert(0,'/global/home/users/muhammad_hasyim/tps-torch/build/')
import scipy.spatial
#Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.examples.dimer_solv_ml import MyMLFTSSampler
from tpsto... | 8,134 | 35.644144 | 122 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/ftme_sl/run_ftsme_sl.py | import sys
sys.path.append("..")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
import scipy.spatial
#Import necessarry tools from tpstorch
from dimer_fts_nosolv import DimerFTS
from committor_nn import CommittorNet, CommittorNetBP, CommittorNe... | 9,052 | 37.198312 | 193 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/us_sl/run_us_sl.py | import sys
sys.path.append("..")
import time
t0 = time.time()
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from dimer_us import DimerUS
from committor_nn import initializeConfig, CommittorNet, CommittorN... | 6,609 | 34.923913 | 181 | py |
tps-torch | tps-torch-main/dimer_solv/ml_test/us_sl/run_us_sl_r.py | import sys
sys.path.append("..")
import time
t0 = time.time()
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from dimer_us import DimerUS
from committor_nn import initializeConfig, CommittorNet, CommittorN... | 7,050 | 35.533679 | 181 | py |
tps-torch | tps-torch-main/muller-brown/committor_test.py | import torch
import numpy as np
import tpstorch.fts as fts
import mullerbrown as mb
# Basically I will read in averaged Voronoi cells, and then determine the committor at the Voronoi cells
committor_vals = np.zeros((32,))
committor_std = np.zeros((32,))
def myprod_checker(config):
end = torch.tensor([[0.5,0.0]])
... | 1,828 | 30 | 104 | py |
tps-torch | tps-torch-main/muller-brown/test.py | import torch
import tpstorch.fts
import mullerbrown as mb
a = mb.MySampler("param",torch.tensor([[0.0,1.0]]),0,0)
#These are just mock tensors
#Intepreat the MD potential as a 2D system for one particle
left_weight = torch.tensor([[1.0,-1.0]])
left_bias = torch.tensor(0.0)
right_weight = torch.tensor([[1.0,-1.0]])
rig... | 417 | 31.153846 | 68 | py |
tps-torch | tps-torch-main/muller-brown/test_vor.py | import torch
import tpstorch.fts as fts
import mullerbrown as mb
import torch.distributed as dist
dist.init_process_group(backend='mpi')
mygroup = dist.distributed_c10d._get_default_group()
rank = dist.get_rank()
#Override FTS class and modify routines as needed
class CustomFTSMethod(fts.FTSMethodVor):
def __init... | 1,539 | 35.666667 | 151 | py |
tps-torch | tps-torch-main/muller-brown/test_fts.py | import torch
import tpstorch.fts as fts
import mullerbrown as mb
import torch.distributed as dist
dist.init_process_group(backend='mpi')
mygroup = dist.distributed_c10d._get_default_group()
rank = dist.get_rank()
#Override FTS class and modify routines as needed
class CustomFTSMethod(fts.FTSMethod):
def __init__(... | 1,384 | 34.512821 | 139 | py |
tps-torch | tps-torch-main/1dbrownian/fts_test/generate_validate.py | #Start up torch dist package
import torch
import torch.distributed as dist
dist.init_process_group(backend='mpi')
#Load classes for simulations and controls
from brownian_fts import BrownianParticle
import numpy as np
#Starting and ending configuration.
start = torch.tensor([[-1.0]])
end = torch.tensor([[1.0]])
def i... | 2,237 | 38.263158 | 138 | py |
tps-torch | tps-torch-main/1dbrownian/fts_test/brownian_fts.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
#Import necessarry tools from tpstorch
#import tpstorch.fts as fts
from tpstorch.fts import FTSSampler, AltFTSMethod
import numpy as np
#Import any other thing
import tqdm, sys
class BrownianParticle(FTSSampler):
def __init__(self... | 3,089 | 38.113924 | 149 | py |
tps-torch | tps-torch-main/1dbrownian/fts_test/run.py | #Start up torch dist package
import torch
import torch.distributed as dist
dist.init_process_group(backend='mpi')
#Load classes for simulations and controls
from brownian_fts import BrownianParticle, CustomFTSMethod
import numpy as np
#Starting and ending configuration.
start = torch.tensor([[-1.0]])
end = torch.tens... | 891 | 33.307692 | 147 | py |
tps-torch | tps-torch-main/1dbrownian/ml_test/brownian_ml_fts.py | #Import necessarry tools from torch
import torch
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml import MLSamplerFTS
from tpstorch.ml.nn import FTSLayer
from tpstorch import dist, _rank, _world_size
from brownian_ml import CommittorNet
import numpy as np
#Import any other thing
import t... | 5,596 | 34.424051 | 148 | py |
tps-torch | tps-torch-main/1dbrownian/ml_test/brownian_ml.py | #Import necessarry tools from torch
import torch
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml import MLSamplerEXP
from tpstorch.ml.nn import FTSLayer
from tpstorch import dist, _rank, _world_size
import numpy as np
#Import any other thing
import tqdm, sys
#The Neural Network for 1D... | 12,395 | 39.37785 | 194 | py |
tps-torch | tps-torch-main/1dbrownian/ml_test/run_vanilla.py | #Import necessarry tools from torch
import torch
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.data import EXPReweightSimulation
from tpstorch.ml.optim import ParallelAdam, ParallelSGD
from tpstorch.ml.nn import BKELossEXP, BKELossFTS
#Import model-specific classes
from brownian_ml im... | 3,912 | 32.732759 | 163 | py |
tps-torch | tps-torch-main/1dbrownian/ml_test/run_cl.py | #Import necessarry tools from torch
import torch
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.data import EXPReweightSimulation
from tpstorch.ml.optim import ParallelAdam, ParallelSGD
from tpstorch.ml.nn import BKELossEXP, BKELossFTS, CommittorLoss2
from brownian_ml import CommittorNe... | 4,611 | 33.939394 | 185 | py |
tps-torch | tps-torch-main/1dbrownian/ml_test/plot.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
import matplotlib.pyplot as plt
import matplotlib as mpl
from matplotlib.ticker import AutoMinorLocator
mpl.rcParams['text.usetex'] = True
params= {'text.latex.preamble' : [r... | 2,752 | 25.728155 | 115 | py |
tps-torch | tps-torch-main/1dbrownian/ml_test/run_fts.py | #Import necessarry tools from torch
import torch
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.data import FTSSimulation
from tpstorch.ml.optim import ParallelAdam, FTSUpdate, ParallelSGD
from tpstorch.ml.nn import BKELossFTS, FTSCommittorLoss, FTSLayer
from brownian_ml_fts import Comm... | 4,850 | 35.473684 | 207 | py |
tps-torch | tps-torch-main/1dbrownian/ml_test/run_fts_cl.py | #Import necessarry tools from torch
import torch
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.data import FTSSimulation
from tpstorch.ml.optim import ParallelAdam, FTSUpdate, ParallelSGD
from tpstorch.ml.nn import BKELossFTS, FTSCommittorLoss, CommittorLoss2, FTSLayer
from brownian_ml... | 5,616 | 35.474026 | 239 | py |
tps-torch | tps-torch-main/muller-brown-ml/mullerbrown_prod.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.optim import project_simplex
from tpstorch.ml import MLSamplerEXP
from tpstorch.ml.nn import CommittorLossEXP
from mul... | 13,332 | 43.591973 | 297 | py |
tps-torch | tps-torch-main/muller-brown-ml/plot_tricky.py | import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.distributed as dist
dist.init_process_group('mpi')
#Import necessarry tools from tpstorch
from mullerbrown import CommittorNet
import numpy as np
#Import any other thing
import tqdm, sys
#Initialize neural net
committor = CommittorNet(d=2,... | 1,485 | 27.037736 | 92 | py |
tps-torch | tps-torch-main/muller-brown-ml/test.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.data import EXPReweightSimulation, TSTValidation
from tpstorch.ml.optim import UnweightedSGD, EXPReweightSGD
from torc... | 6,259 | 35.823529 | 171 | py |
tps-torch | tps-torch-main/muller-brown-ml/mb_fts.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.examples.mullerbrown_ml import MyMLFTSSampler
from tpstorch import _rank, _world_size
import numpy as np
#Import any other thing
import tqdm, sys
#A single hi... | 4,992 | 32.965986 | 108 | py |
tps-torch | tps-torch-main/muller-brown-ml/mullerbrown.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.optim import project_simplex
from tpstorch.ml import MLSamplerEXP
from tpstorch.ml.nn import CommittorLossEXP
from mul... | 4,508 | 36.264463 | 121 | py |
tps-torch | tps-torch-main/muller-brown-ml/run_fts_c.py | #import sys
#sys.path.insert(0,"/global/home/users/muhammad_hasyim/tps-torch/build")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from mb_fts import MullerBrown, CommittorNet
from tpstorch.ml.data import... | 6,959 | 38.101124 | 239 | py |
tps-torch | tps-torch-main/muller-brown-ml/test_sampler_2.py | import mullerbrown_ml as mb
import torch
import torch.distributed as dist
from torch.distributed import distributed_c10d
dist.init_process_group(backend='mpi')
mpi_group = dist.distributed_c10d._get_default_group()
a = mb.MySampler('param_tst',torch.tensor([[0.5,0.5]]),0,0,2.0,0.0,distributed_c10d._get_default_group... | 504 | 30.5625 | 105 | py |
tps-torch | tps-torch-main/muller-brown-ml/run_fts_c2.py | #import sys
#sys.path.insert(0,"/global/home/users/muhammad_hasyim/tps-torch/build")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from mb_fts import MullerBrown, CommittorNet
from tpstorch.ml.data import... | 7,612 | 39.068421 | 271 | py |
tps-torch | tps-torch-main/muller-brown-ml/run_vanilla.py | #import sys
#sys.path.insert(0,"/global/home/users/muhammad_hasyim/tps-torch/build")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from mb_ml import MullerBrown, CommittorNet
from tpstorch.ml.data import ... | 5,494 | 36.128378 | 180 | py |
tps-torch | tps-torch-main/muller-brown-ml/test_sampler.py | import mullerbrown_ml as mb
import torch
import torch.distributed as dist
dist.init_process_group(backend='mpi')
mpi_group = dist.distributed_c10d._get_default_group()
a = mb.MySampler('param',torch.tensor([[0.0,0.0]]),0,0,0.0,0.0,dist.distributed_c10d._get_default_group())
| 277 | 29.888889 | 106 | py |
tps-torch | tps-torch-main/muller-brown-ml/plot_tricky_string.py | import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.distributed as dist
#Import necessarry tools from tpstorch
from mb_fts import CommittorNet
from tpstorch.ml.nn import FTSLayer
import numpy as np
#Import any other thing
import tqdm, sys
#Initialize neural net
committor = CommittorNet(d=2,... | 1,831 | 29.032787 | 92 | py |
tps-torch | tps-torch-main/muller-brown-ml/run_cl.py | #import sys
#sys.path.insert(0,"/global/home/users/muhammad_hasyim/tps-torch/build")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from mb_ml import MullerBrown, CommittorNet
from tpstorch.ml.data import ... | 6,208 | 37.565217 | 185 | py |
tps-torch | tps-torch-main/muller-brown-ml/test_prod.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.data import EXPReweightSimulation, EXPReweightSimulationManual, TSTValidation
from tpstorch.ml.optim import Unweighted... | 10,128 | 39.678715 | 401 | py |
tps-torch | tps-torch-main/muller-brown-ml/plot.py | import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.distributed as dist
dist.init_process_group('mpi')
#Import necessarry tools from tpstorch
from mullerbrown import CommittorNet
import numpy as np
#Import any other thing
import tqdm, sys
#Initialize neural net
committor = CommittorNet(d=2,... | 1,220 | 22.037736 | 84 | py |
tps-torch | tps-torch-main/muller-brown-ml/mb_ml.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml import MLSamplerEXP
from tpstorch.examples.mullerbrown_ml import MyMLSampler
import numpy as np
#Import any other thi... | 4,567 | 33.345865 | 108 | py |
tps-torch | tps-torch-main/muller-brown-ml/mullerbrown_tricky.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.optim import project_simplex
from tpstorch.ml import MLSamplerEXP
from tpstorch.ml.nn import CommittorLossEXP
from mul... | 4,466 | 36.225 | 104 | py |
tps-torch | tps-torch-main/muller-brown-ml/run_fts.py | #import sys
#sys.path.insert(0,"/global/home/users/muhammad_hasyim/tps-torch/build")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from mb_fts import MullerBrown, CommittorNet
from tpstorch.ml.data import... | 6,865 | 37.79096 | 239 | py |
tps-torch | tps-torch-main/muller-brown-ml/test_tricky.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.data import EXPReweightSimulation, EXPReweightSimulationManual, TSTValidation
from tpstorch.ml.optim import Unweighted... | 7,966 | 38.835 | 213 | py |
tps-torch | tps-torch-main/muller-brown-ml/mullerbrown_relu.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.optim import project_simplex
from tpstorch.ml import MLSamplerEXP
from tpstorch.ml.nn import CommittorLossEXP
from mul... | 5,015 | 37.290076 | 121 | py |
tps-torch | tps-torch-main/muller-brown-ml/test_relu.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.data import EXPReweightSimulation, TSTValidation
from tpstorch.ml.optim import UnweightedSGD, EXPReweightSGD
from torc... | 7,861 | 38.114428 | 213 | py |
tps-torch | tps-torch-main/muller-brown-ml/mrh_tests/mb_fts.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.examples.mullerbrown_ml import MyMLFTSSampler
from tpstorch import _rank, _world_size
import numpy as np
#Import any other thing
import tqdm, sys
#A single hi... | 4,995 | 32.986395 | 108 | py |
tps-torch | tps-torch-main/muller-brown-ml/mrh_tests/run_vanilla.py | #Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from mb_ml import MullerBrown, CommittorNet
from tpstorch.ml.data import EXPReweightSimulation
from tpstorch.ml.optim import ParallelSGD, ParallelAdam
from tps... | 5,413 | 36.337931 | 180 | py |
tps-torch | tps-torch-main/muller-brown-ml/mrh_tests/mb_ml.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml import MLSamplerEXP
from tpstorch.examples.mullerbrown_ml import MyMLSampler
import numpy as np
#Import any other thing
import tqdm, sys
#dist.init_process_... | 4,527 | 33.30303 | 108 | py |
tps-torch | tps-torch-main/muller-brown-ml/mrh_tests/run_fts.py | #import sys
#sys.path.insert(0,"/global/home/users/muhammad_hasyim/tps-torch/build")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from mb_fts import MullerBrown, CommittorNet
from tpstorch.ml.data import... | 7,051 | 39.068182 | 240 | py |
tps-torch | tps-torch-main/muller-brown-ml/examples/0/mullerbrown.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.optim import project_simplex
from tpstorch.ml import MLSamplerEXP
from tpstorch.ml.nn import CommittorLossEXP
from mul... | 4,579 | 36.235772 | 104 | py |
tps-torch | tps-torch-main/muller-brown-ml/examples/0/run.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.data import EXPReweightSimulation, TSTValidation
from tpstorch.ml.optim import UnweightedSGD, EXPReweightSGD
from torc... | 6,698 | 36.216667 | 175 | py |
tps-torch | tps-torch-main/muller-brown-ml/examples/2/mullerbrown.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.optim import project_simplex
from tpstorch.ml import MLSamplerEXP
from tpstorch.ml.nn import CommittorLossEXP
from mul... | 4,466 | 36.225 | 104 | py |
tps-torch | tps-torch-main/muller-brown-ml/examples/2/run.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.data import EXPReweightSimulation, TSTValidation
from tpstorch.ml.optim import UnweightedSGD, EXPReweightSGD
from torc... | 6,699 | 36.222222 | 175 | py |
tps-torch | tps-torch-main/muller-brown-ml/examples/1/mullerbrown.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.optim import project_simplex
from tpstorch.ml import MLSamplerEXP
from tpstorch.ml.nn import CommittorLossEXP
from mul... | 4,466 | 36.225 | 104 | py |
tps-torch | tps-torch-main/muller-brown-ml/examples/1/run.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.ml.data import EXPReweightSimulation, TSTValidation
from tpstorch.ml.optim import UnweightedSGD, EXPReweightSGD
from torc... | 6,699 | 36.222222 | 175 | py |
tps-torch | tps-torch-main/muller-brown-ml/analysis_scripts/plot_tricky_2.py | import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.distributed as dist
from torch.autograd import grad
#Import necessarry tools from tpstorch
from mb_ml import CommittorNet
import numpy as np
#Import any other thing
import tqdm, sys
#Initialize neural net
committor = CommittorNet(d=2,num_n... | 2,969 | 31.637363 | 100 | py |
tps-torch | tps-torch-main/muller-brown-ml/analysis_scripts/plot_tricky.py | import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.distributed as dist
dist.init_process_group('mpi')
#Import necessarry tools from tpstorch
from mullerbrown import CommittorNet
import numpy as np
#Import any other thing
import tqdm, sys
#Initialize neural net
committor = CommittorNet(d=2,... | 1,507 | 27.45283 | 106 | py |
tps-torch | tps-torch-main/muller-brown-ml/analysis_scripts/plot_tricky_string_2.py | import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.distributed as dist
from torch.autograd import grad
#Import necessarry tools from tpstorch
from mb_fts import CommittorNet
from tpstorch.ml.nn import FTSLayer
import numpy as np
#Import any other thing
import tqdm, sys
#Initialize neural n... | 3,195 | 32.291667 | 100 | py |
tps-torch | tps-torch-main/muller-brown-ml/analysis_scripts/plot_tricky_t.py | import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.distributed as dist
dist.init_process_group('mpi')
#Import necessarry tools from tpstorch
from mullerbrown import CommittorNet
import numpy as np
#Import any other thing
import tqdm, sys
#Initialize neural net
committor = CommittorNet(d=2,... | 1,511 | 27.528302 | 106 | py |
tps-torch | tps-torch-main/muller-brown-ml/analysis_scripts/plot_tricky_string.py | import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.distributed as dist
#Import necessarry tools from tpstorch
from mb_fts import CommittorNet
from tpstorch.ml.nn import FTSLayer
import numpy as np
#Import any other thing
import tqdm, sys
#Initialize neural net
committor = CommittorNet(d=2,... | 1,831 | 29.032787 | 92 | py |
tps-torch | tps-torch-main/muller-brown-ml/analysis_scripts/energies.py | import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.distributed as dist
from torch.autograd import grad
#Import necessarry tools from tpstorch
from mb_ml import CommittorNet
import numpy as np
#Import any other thing
import tqdm, sys
#Initialize neural net
committor = CommittorNet(d=2,num_n... | 2,741 | 31.258824 | 93 | py |
tps-torch | tps-torch-main/tpstorch/__init__.py | #Always initialize MPI when importing this module
import torch
import torch.distributed as dist
dist.init_process_group(backend='mpi')
#Save the MPI group, rank, and size
_mpi_group = dist.distributed_c10d._get_default_group()
_rank = dist.get_rank()
_world_size = dist.get_world_size()
from . import _tpstorch
from . ... | 2,980 | 40.985915 | 111 | py |
tps-torch | tps-torch-main/tpstorch/fts/__init__.py | import tpstorch
import torch
import torch.distributed as dist
from tpstorch.fts import _fts
#A class that interfaces with an existing MD/MC code. Its main job is to streamline
#An existing MD code with an FTS method Class.
class FTSSampler(_fts.FTSSampler):
pass
#Class for Handling Finite-Temperature String Met... | 25,508 | 50.742394 | 178 | py |
tps-torch | tps-torch-main/tpstorch/examples/mullerbrown_ml/__init__.py | from tpstorch.ml import _ml
from . import _mullerbrown_ml
#Just something to pass the class
class MyMLSampler(_mullerbrown_ml.MySampler):
pass
#Just something to pass the class
class MyMLEXPStringSampler(_mullerbrown_ml.MySamplerEXPString):
pass
#Just something to pass the class
class MyMLFTSSampler(_mullerbr... | 351 | 24.142857 | 63 | py |
tps-torch | tps-torch-main/tpstorch/examples/dimer_ml/__init__.py | from tpstorch.ml import _ml
from . import _dimer_ml
#Just something to pass the class
class MyMLEXPSampler(_dimer_ml.DimerEXP):
pass
class MyMLEXPStringSampler(_dimer_ml.DimerEXPString):
pass
class MyMLFTSSampler(_dimer_ml.DimerFTS):
pass
| 254 | 18.615385 | 53 | py |
tps-torch | tps-torch-main/tpstorch/examples/dimer_solv_ml/__init__.py | from tpstorch.ml import _ml
from . import _dimer_solv_ml
#Just something to pass the class
class MyMLEXPSampler(_dimer_solv_ml.DimerSolvEXP):
pass
class MyMLEXPStringSampler(_dimer_solv_ml.DimerSolvEXPString):
pass
class MyMLFTSSampler(_dimer_solv_ml.DimerSolvFTS):
pass
| 286 | 21.076923 | 62 | py |
tps-torch | tps-torch-main/tpstorch/ml/deprecated.py | """
A place to put classes and method which we will discard for all future implementations. We'll still include in case we want to revert back
"""
import torch
from torch.optim import Optimizer
from torch.optim.optimizer import required
from torch.utils.data import IterableDataset
import torch.distributed as dist
impo... | 14,663 | 43.302115 | 186 | py |
tps-torch | tps-torch-main/tpstorch/ml/optim.py | import torch
from torch.optim import Optimizer
from torch.optim.optimizer import required
from tpstorch import _rank, _world_size
from tpstorch import dist
# Stolen adam implementation from PyTorch, weird *, operator kills us everytime
import math
from torch import Tensor
from typing import List, Optional
def adam(pa... | 20,999 | 43.680851 | 170 | py |
tps-torch | tps-torch-main/tpstorch/ml/data.py | import torch
import numpy as np
from tpstorch import _rank, _world_size
class FTSSimulation:
def __init__(self, sampler, batch_size, dimN, period=10,mode='nonadaptive', committor = None, nn_training=True,**kwargs):#, nn_training=True):
## Store the MD/MC Simulator, which samples our data
self.sampl... | 17,425 | 41.921182 | 157 | py |
tps-torch | tps-torch-main/tpstorch/ml/nn.py | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
from torch.nn.modules.loss import _Loss
#import scipy.sparse.linalg
from tpstorch import _rank, _world_size
from tpstorch import dist
from numpy.linalg import svd
import scipy.linalg
#Helper function to obtain null space
def nul... | 64,002 | 44.586182 | 212 | py |
tps-torch | tps-torch-main/tpstorch/ml/__init__.py | from . import _ml, optim, nn, data
from tpstorch import _mpi_group
#Inherit the C++ compiled sampler class, and add the MPI process group by default
class MLSamplerEXP(_ml.MLSamplerEXP):
def __init__(self, initial_config):
super(MLSamplerEXP,self).__init__(initial_config, _mpi_group)
#Inherit the C++ comp... | 1,030 | 43.826087 | 81 | py |
tps-torch | tps-torch-main/dimer/fts_test/dimer_fts.py | import sys
sys.path.insert(0,'/global/home/users/muhammad_hasyim/tps-torch/build/')
#Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.examples.dimer_ml import MyMLFTSSampler
from tpstorch import _rank, _world_s... | 7,580 | 34.425234 | 118 | py |
tps-torch | tps-torch-main/dimer/fts_test/fts_simulation.py | #import sys
#sys.path.insert(0,"/global/home/users/muhammad_hasyim/tps-torch/build")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
#from mb_fts import MullerBrown as MullerBrownFTS#, CommittorNet
from dim... | 5,130 | 33.206667 | 207 | py |
tps-torch | tps-torch-main/dimer/ml_test/nn_initialization.py | #import sys
#sys.path.insert(0,"/global/home/users/muhammad_hasyim/tps-torch/build")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from dimer_ftsus import FTSLayerUSCustom as FTSLayer
from committor_nn im... | 3,069 | 29.7 | 156 | py |
tps-torch | tps-torch-main/dimer/ml_test/plotmodel.py | #Import necessarry tools from torch
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader
import torch.nn as nn
#Import necessarry tools from tpstorch
#from brownian_ml import CommittorNet
from committor_nn import CommittorNet, CommittorNetDR
import numpy as np
#Import any other thing... | 1,397 | 22.694915 | 82 | py |
tps-torch | tps-torch-main/dimer/ml_test/committor_nn.py | #Import necessarry tools from torch
import torch
import torch.nn as nn
import numpy as np
#Import any other thing
import tqdm, sys
class CommittorNet(nn.Module):
def __init__(self, d, num_nodes, unit=torch.relu):
super(CommittorNet, self).__init__()
self.num_nodes = num_nodes
self.d = d
... | 2,015 | 28.647059 | 62 | py |
tps-torch | tps-torch-main/dimer/ml_test/ftsme/dimer_fts.py | import sys
sys.path.insert(0,'/global/home/users/muhammad_hasyim/tps-torch/build/')
#Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.examples.dimer_ml import MyMLFTSSampler
from tpstorch import _rank, _world_s... | 7,906 | 34.457399 | 118 | py |
tps-torch | tps-torch-main/dimer/ml_test/ftsme/run_ftsme.py | import sys
sys.path.append("..")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from dimer_fts import DimerFTS
from committor_nn import CommittorNet, CommittorNetDR
from dimer_fts import FTSLayerCustom as ... | 6,330 | 34.768362 | 210 | py |
tps-torch | tps-torch-main/dimer/ml_test/ftsus/run_ftsus.py | import sys
sys.path.append("..")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from dimer_ftsus import DimerFTSUS
from committor_nn import CommittorNet, CommittorNetDR
from dimer_ftsus import FTSLayerUSCu... | 4,082 | 32.195122 | 225 | py |
tps-torch | tps-torch-main/dimer/ml_test/ftsus/dimer_ftsus.py | import sys
sys.path.insert(0,'/global/home/users/muhammad_hasyim/tps-torch/build/')
#Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.examples.dimer_ml import MyMLEXPStringSampler
from tpstorch import _rank, _w... | 10,322 | 36.538182 | 142 | py |
tps-torch | tps-torch-main/dimer/ml_test/us/dimer_us.py | import sys
sys.path.insert(0,'/global/home/users/muhammad_hasyim/tps-torch/build/')
#Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.examples.dimer_ml import MyMLEXPSampler
from tpstorch import _rank, _world_s... | 4,046 | 32.172131 | 107 | py |
tps-torch | tps-torch-main/dimer/ml_test/us/run_us.py | import sys
sys.path.append("..")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from dimer_us import DimerUS
from committor_nn import CommittorNetDR
from tpstorch.ml.data import EXPReweightSimulation
from ... | 3,591 | 29.700855 | 187 | py |
tps-torch | tps-torch-main/dimer/ml_test/ftsus_sl/dimer_ftsus.py | import sys
sys.path.insert(0,'/global/home/users/muhammad_hasyim/tps-torch/build/')
#Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.examples.dimer_ml import MyMLEXPStringSampler
from tpstorch import _rank, _w... | 10,322 | 36.538182 | 142 | py |
tps-torch | tps-torch-main/dimer/ml_test/ftsus_sl/run_ftsus_sl.py | import sys
sys.path.append("..")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from dimer_ftsus import DimerFTSUS
from committor_nn import CommittorNet, CommittorNetDR
from dimer_ftsus import FTSLayerUSCu... | 5,023 | 33.176871 | 225 | py |
tps-torch | tps-torch-main/dimer/ml_test/ftsme_sl/dimer_fts.py | import sys
sys.path.insert(0,'/global/home/users/muhammad_hasyim/tps-torch/build/')
#Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.examples.dimer_ml import MyMLFTSSampler
from tpstorch import _rank, _world_s... | 7,906 | 34.457399 | 118 | py |
tps-torch | tps-torch-main/dimer/ml_test/ftsme_sl/run_ftsme_sl.py | import sys
sys.path.append("..")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from dimer_fts import DimerFTS
from committor_nn import CommittorNet, CommittorNetDR
from dimer_fts import FTSLayerCustom as ... | 7,300 | 35.323383 | 210 | py |
tps-torch | tps-torch-main/dimer/ml_test/us_sl/dimer_us.py | import sys
sys.path.insert(0,'/global/home/users/muhammad_hasyim/tps-torch/build/')
#Import necessarry tools from torch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from tpstorch.examples.dimer_ml import MyMLEXPSampler
from tpstorch import _rank, _world_s... | 4,046 | 32.172131 | 107 | py |
tps-torch | tps-torch-main/dimer/ml_test/us_sl/run_us_sl.py | import sys
sys.path.append("..")
#Import necessarry tools from torch
import tpstorch
import torch
import torch.distributed as dist
import torch.nn as nn
#Import necessarry tools from tpstorch
from dimer_us import DimerUS
from committor_nn import CommittorNetDR
from tpstorch.ml.data import EXPReweightSimulation
from ... | 4,555 | 31.542857 | 187 | py |
AutoAE | AutoAE-master/attack_ops.py | import numpy as np
from itertools import product, repeat
import PIL
import torch
import torch.nn as nn
from torch.autograd import Variable
from torch.nn import functional as F
from torchvision import transforms
from tv_utils import SpatialAffine, GaussianSmoothing
from attack_utils import projection_linf, check_shape, ... | 96,677 | 40.017395 | 212 | py |
AutoAE | AutoAE-master/get_robust_accuracy_by_AutoAE.py |
import sys
import os
os.environ["CUDA_VISIBLE_DEVICES"] = "0"
import torch
import torch.nn as nn
from torch.nn import functional as F
from PIL import Image
import numpy as np
import torchvision
import imageio
from torchvision import transforms
import argparse
from attack_ops import apply_attacker
from tqdm import tq... | 12,604 | 41.728814 | 175 | py |
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