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Update ACE run-experiments.jl and documentation.
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‎docs/src/index.md

+30-29
Original file line numberDiff line numberDiff line change
@@ -77,12 +77,12 @@ The input parameters are listed below:
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| Input parameter | Description | E.g. |
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|----------------------|-----------------------------------------------------------|---------------------|
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| experiment_path | Experiment path | TiO2/ |
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| experiment_path | Experiment path | HfB2/ |
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| dataset_path | Dataset path | data/ |
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| trainingset_filename | Training datasets filename | TiO2trainingset.xyz |
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| testset_filename | Test datasets filename | TiO2testset.xyz |
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| n_train_sys | No. of atomic configurations in training dataset | 80 |
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| n_test_sys | No. of atomic configurations in test dataset | 20 |
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| dataset_filename | Dataset filename | HfB2-n24-585.exyz |
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| split_prop | Split proportion. E.g. 0.8 training, 0.2 test. | 0.8 |
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| max_train_sys | Max. no. of atomic systems in training dataset | 800 |
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| max_test_sys | No. of atomic systems in test dataset | 200 |
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| n_body | Body order | 3 |
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| max_deg | Maximum polynomial degree | 3 |
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| r0 | An estimate on the nearest-neighbour distance for scaling | 1.0 |
@@ -92,29 +92,30 @@ The input parameters are listed below:
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| w_e | Energy weight | 1.0 |
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| w_f | Force weight | 1.0 |
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Run fitting process
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```shell
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$ julia fit-ace.jl experiment_path TiO2/ \
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dataset_path data/ \
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trainingset_filename TiO2trainingset.xyz \
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testset_filename TiO2testset.xyz \
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n_train_sys 80 \
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n_test_sys 20 \
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n_body 3 \
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max_deg 3 \
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r0 1.0 \
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rcutoff 5.0 \
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wL 1.0 \
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csp 1.0 \
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w_e 1.0 \
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w_f 1.0
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$ julia --project=../../ fit-ace.jl experiment_path HfB2/ \
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dataset_path ../../../data/ \
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dataset_filename HfB2-n24-585.exyz \
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split_prop 0.8 \
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max_train_sys 800 \
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max_test_sys 200 \
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n_body 3 \
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max_deg 3 \
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r0 1.0 \
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rcutoff 5.0 \
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wL 1.0 \
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csp 1.0 \
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w_e 1.0 \
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w_f 1.0
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```
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In addition, you can run the experiments with the default parameters (the parameters shown above).
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```shell
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$ julia fit-ace.jl
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$ julia --project=../../ fit-ace.jl
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```
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### Run multiple fitting experiments in serial/parallel using the wrapper to ACE1.jl in InteratomicBasisPotentials.jl
@@ -134,7 +135,7 @@ Modify the file `run-experiments.jl` to specify the parameter ranges needed to g
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Run the script:
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```shell
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$ julia run-experiments.jl
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$ julia --project=../../ run-experiments.jl
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```
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Each experiment is run in a separate process (using `nohup` to facilitate its execution in a cluster).
@@ -148,11 +149,11 @@ After all experiments have been completed, run the following script to gather th
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### Run an MD simulation using the wrapper to Molly.jl or NBodySimulator.jl in Atomistic.jl
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```shell
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$ run-md-ahfo2-ace-nbs.jl
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$ julia --project=../../ run-md-ahfo2-ace-nbs.jl
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```
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or
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```shell
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$ run-md-ahfo2-ace-molly.jl
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$ julia --project=../../ run-md-ahfo2-ace-molly.jl
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```
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(Note: currently there is a bug in the second script)
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@@ -166,21 +167,21 @@ or
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Open terminal and download Julia from https://julialang.org/downloads/
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```shell
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$ wget https://julialang-s3.julialang.org/bin/linux/x64/1.7/julia-1.7.3-linux-x86_64.tar.gz
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$ wget https://julialang-s3.julialang.org/bin/linux/x64/1.8/julia-1.8.0-linux-x86_64.tar.gz
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```
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Extract file
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```shell
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$ tar xvzf julia-1.7.3-linux-x86_64.tar.gz
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$ tar xvzf julia-1.8.0-linux-x86_64.tar.gz
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```
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Copy to `/opt` and create link
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```shell
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$ sudo mv ./julia-1.7.3 /opt/
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$ sudo ln -s /opt/julia-1.7.3/bin/julia /usr/local/bin/julia
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$ sudo mv ./julia-1.8.0 /opt/
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$ sudo ln -s /opt/julia-1.8.0/bin/julia /usr/local/bin/julia
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```
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Alternative: add line to `.shellrc`
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```shell
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$ nano .shellrc
183-
PATH=$PATH:/home/youruser/julia-1.7.3 /bin/
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PATH=$PATH:/home/youruser/julia-1.8.0 /bin/
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```
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Restart the terminal
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@@ -204,4 +205,4 @@ Activate and instantiate
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```julia
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pkg> activate .
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pkg> instantiate
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```
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```

‎workflows/ACE/fit-ace.jl

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ using LinearAlgebra
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# Load input parameters
9-
args = ["experiment_path", "HfB2-33/",
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args = ["experiment_path", "HfB2/",
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"dataset_path", "../../../data/",
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"dataset_filename", "HfB2-n24-585.exyz",
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"split_prop", "0.8", # 80% training, 20% test.

‎workflows/ACE/run-experiments.jl

+29-30
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
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# Run multiple fitting experiments in serial or parallel.
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#
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# 1. Update parameters ranges in run-experiments.jl
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# 2. Run: $ julia run-experiments.jl
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# 2. Run: $ julia --project=../../ run-experiments.jl
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# 3. After all experiments have been completed, run the following script to gather
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# the results into a single csv: $ ./gather-results.sh
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#
@@ -11,11 +11,10 @@ using IterTools
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# Parameter labels
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labels = [ "experiment_path",
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"dataset_path",
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"trainingset_filename",
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"testset_filename",
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"n_train_sys",
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"n_test_sys",
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"n_batches",
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"dataset_filename",
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"split_prop",
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"max_train_sys",
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"max_test_sys",
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"n_body",
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"max_deg",
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"r0",
@@ -25,9 +24,8 @@ labels = [ "experiment_path",
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"w_e",
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"w_f"]
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# Parallel execution. Warning: a high number of parallel experiments may degrade system performance.
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parallel = false
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parallel = true
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# Experiment folder
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experiments_path = "experiments/"
@@ -38,25 +36,27 @@ juliafile = "fit-ace.jl"
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# Parameter definitions ########################################################
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# dataset path
41-
dataset_path = ["../data/"]
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dataset_path = ["../../../data/"]
40+
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# dataset filename
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dataset_filename = [ "HfB2-n24-585.exyz",
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"HfO2_cpmd_1000.xyz",
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"HfO2_cpmd_train_0_94_11_7700.xyz",
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"HfO2_relax_1000_989.xyz" ]
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43-
# datasets filename
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trainingset_filename = ["TiO2trainingset.xyz"]
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testset_filename = ["TiO2testset.xyz"]
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# Split proportoin
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split_prop = 0.8:0.8
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# number of atomic configurations
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#n_systems = 100:100
49-
n_train_sys = 80:80
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n_test_sys = 20:20
51+
max_train_sys = 800:800
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max_test_sys = 200:200
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52-
# number of batches per dataset
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n_batches = 8:8
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# n_body: body order. N: correlation order (N = n_body - 1)
56-
n_body = 2:5
56+
n_body = 2:2
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# max_deg: maximum polynomial degree
59-
max_deg = 3:6
59+
max_deg = 3:3
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# r0: An estimate on the nearest-neighbour distance for scaling, JuLIP.rnn()
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# function returns element specific earest-neighbour distance
@@ -66,43 +66,42 @@ r0 = 1.0:1.0 # ( rnn(:Hf) + rnn(:O) ) / 2.0 ?
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# rin = 0.65*r0 is the default
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# rcutoff or rcut: outer cutoff radius
69-
rcutoff = 4.0:7.0
69+
rcutoff = 5.0:5.0
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# D: specifies the notion of polynomial degree for which there is no canonical
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# definition in the multivariate setting. Here we use SparsePSHDegree which
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# specifies a general class of sparse basis sets; see its documentation for
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# more details. Default: D = ACE1.SparsePSHDegree(; wL = rpi.wL, csp = rpi.csp)
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# wL: ?
76-
wL = 0.5:0.5:1.5
76+
wL = 1.0:1.0
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# csp: ?
78-
csp = 0.5:0.5:1.5
78+
csp = 1.0:1.0
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# pin: specifies the behaviour of the basis as the inner cutoff radius.
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# pin = 0 is the default.
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8383
# w_e: energy weight, used during fitting in normal equations
84-
w_e = [1e-8, 1.0, 100.0]
84+
w_e = 1.0:1.0
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8686
# w_f: force weight, used during fitting in normal equations
87-
w_f = [1e-8, 1.0, 100.0]
87+
w_f = 1.0:1.0
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8989

9090
# Run experiments ##############################################################
9191

92-
run(`mkdir $experiments_path`)
93-
for params in product(dataset_path, trainingset_filename, testset_filename,
94-
n_train_sys, n_test_sys, n_batches,
95-
n_body, max_deg, r0, rcutoff, wL, csp, w_e, w_f)
92+
run(`mkdir -p $experiments_path`)
93+
for params in product( dataset_path, dataset_filename, split_prop, max_train_sys,
94+
max_test_sys, n_body, max_deg, r0, rcutoff, wL, csp, w_e, w_f)
9695
print("Launching experiment with parameters: ")
9796
currexp_path = reduce(*,map(s->"$s"*"-", params[2:end]))[1:end-1]
9897
params = vcat(["$(labels[1])", "$experiments_path$currexp_path/"],
9998
vcat([ ["$l", "$p"] for (l, p) in zip(labels[2:end], params)]...))
10099
println("$params")
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102101
if parallel
103-
@async run(Cmd(`nohup julia $juliafile $params`, dir="./"));
102+
@async run(Cmd(`nohup julia --project=../../ $juliafile $params`, dir="./"));
104103
else
105-
run(Cmd(`julia $juliafile $params`, dir="./"));
104+
run(Cmd(`julia --project=../../ $juliafile $params`, dir="./"));
106105
end
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108107
println("")

‎workflows/NeuralACE-experimental/run-experiments.jl

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@@ -1,7 +1,7 @@
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# Run multiple fitting experiments in serial or parallel.
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#
33
# 1. Update parameters ranges in run-experiments.jl
4-
# 2. Run: $ julia run-experiments.jl
4+
# 2. Run: $ julia --project=../../ run-experiments.jl
55
# 3. After all experiments have been completed, run the following script to gather
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# the results into a single csv: $ ./gather-results.sh
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#
@@ -41,10 +41,13 @@ juliafile = "fit-neural-ace.jl"
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# Parameter definitions ########################################################
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4343
# dataset path
44-
dataset_path = ["../../data/"]
44+
dataset_path = ["../../../data/"]
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4646
# dataset filename
47-
dataset_filename = ["HfB2-n24-585.exyz"]
47+
dataset_filename = [ "HfO2_cpmd_1000.xyz",
48+
"HfO2_cpmd_train_0_94_11_7700.xyz",
49+
"HfO2_relax_1000_989.xyz",
50+
"HfB2-n24-585.exyz"]
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4952
# Split proportoin
5053
split_prop = 0.8:0.8
@@ -63,7 +66,7 @@ n_batches = 1:1
6366
optimiser = ["BFGS"]
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6568
# Max. no. of optimizer iterations
66-
max_it = 70:70
69+
max_it = 100:100
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6871
# n_body: body order. N: correlation order (N = n_body - 1)
6972
n_body = 2:2

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