Merge pull request #2641 from pedroantoniosantosf/mliap_nn
Add support for neural network (nn) models to MLIAP package to compute energies and forces without going through Python
This commit is contained in:
Axel Kohlmeyer
@ -16,7 +16,7 @@ Syntax
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.. parsed-literal::
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*model* values = style filename
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style = *linear* or *quadratic* or *mliappy*
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style = *linear* or *quadratic* or *nn* or *mliappy*
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filename = name of file containing model definitions
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*descriptor* values = style filename
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style = *sna*
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@ -45,7 +45,7 @@ pair style currently supports just one descriptor style, but it is
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is straightforward to add new descriptor styles.
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The SNAP descriptor style *sna* is the same as that used by :doc:`pair_style snap <pair_snap>`,
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including the linear, quadratic, and chem variants.
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The available models are *linear*, *quadratic*, and *mliappy*.
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The available models are *linear*, *quadratic*, *nn*, and *mliappy*.
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The *mliappy* style can be used to couple python models,
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e.g. PyTorch neural network energy models, and requires building
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LAMMPS with the PYTHON package (see below).
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@ -77,13 +77,32 @@ line must contain two integers:
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* nelems = Number of elements
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* nparams = Number of parameters
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This is followed by one block for each of the *nelem* elements.
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When the *model* keyword is *linear* or *quadratic*,
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this is followed by one block for each of the *nelem* elements.
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Each block consists of *nparams* parameters, one per line.
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Note that this format is similar, but not identical to that used
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for the :doc:`pair_style snap <pair_snap>` coefficient file.
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Specifically, the line containing the element weight and radius is omitted,
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since these are handled by the *descriptor*.
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When the *model* keyword is *nn* (neural networks), the model file can contain
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blank and comment lines (start with #) anywhere. The second non-blank non-comment
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line must contain the string NET, followed by two integers:
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* ndescriptors = Number of descriptors
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* nlayers = Number of layers (including the hidden layers and the output layer)
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and followed by a sequence of a string and an integer for each layer:
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* Activation function (linear, sigmoid, tanh or relu)
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* nnodes = Number of nodes
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This is followed by one block for each of the *nelem* elements. Each block consists
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of *scale0* minimum value, *scale1* (maximum - minimum) value,
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in order to normalize the descriptors, followed by *nparams* parameters,
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including *bias* and *weights* of the model, starting with the first node of the first layer
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and so on, with a maximum of 30 values per line.
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Notes on mliappy models:
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When the *model* keyword is *mliappy*, the filename should end in '.pt',
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'.pth' for pytorch models, or be a pickle file. To load a model from
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@ -2098,6 +2098,7 @@ ncol
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ncorr
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ncount
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nd
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ndescriptors
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ndihedrals
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ndihedraltypes
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Ndihedraltype
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@ -2158,6 +2159,7 @@ niu
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Nk
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nktv
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nl
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nlayers
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nlen
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Nlines
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nlo
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@ -2173,6 +2175,7 @@ Nmin
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nmin
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Nmols
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nn
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nnodes
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Nocedal
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nocite
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nocoeff
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@ -2659,6 +2662,7 @@ relaxbox
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relink
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relres
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relTol
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relu
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remappings
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remd
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Ren
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@ -2888,6 +2892,7 @@ si
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SiC
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Siepmann
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Sievers
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sigmoid
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Sij
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Sikandar
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Silbert
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1
examples/mliap/Cu.nn.mliap.model
Symbolic link
1
examples/mliap/Cu.nn.mliap.model
Symbolic link
@ -0,0 +1 @@
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../../potentials/Cu.nn.mliap.model
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1
examples/mliap/Cu.snap.mliap.descriptor
Symbolic link
1
examples/mliap/Cu.snap.mliap.descriptor
Symbolic link
@ -0,0 +1 @@
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../../potentials/Cu.snap.mliap.descriptor
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@ -101,3 +101,12 @@ pickle data that will execute arbitrary code during unpickling. Never
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load data that could have come from an untrusted source, or that
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could have been tampered with. Only load data you trust.
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in.mliap.nn.Ta06A
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-------------------
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Run linear SNAP using the "nn" model style, equivalent to examples/snap/in.snap.Ta06A
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in.mliap.nn.cu
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-------------------------
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Run a neural network potential for Cu, a combination of SNAP descriptors and the "nn" model style
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1
examples/mliap/Ta06A.nn.mliap
Symbolic link
1
examples/mliap/Ta06A.nn.mliap
Symbolic link
@ -0,0 +1 @@
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../../potentials/Ta06A.nn.mliap
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1
examples/mliap/Ta06A.nn.mliap.model
Symbolic link
1
examples/mliap/Ta06A.nn.mliap.model
Symbolic link
@ -0,0 +1 @@
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../../potentials/Ta06A.nn.mliap.model
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1
examples/mliap/Ta06A.pytorch.mliap
Symbolic link
1
examples/mliap/Ta06A.pytorch.mliap
Symbolic link
@ -0,0 +1 @@
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../../potentials/Ta06A.pytorch.mliap
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53
examples/mliap/in.mliap.nn.Cu
Normal file
53
examples/mliap/in.mliap.nn.Cu
Normal file
@ -0,0 +1,53 @@
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# Demonstrate MLIAP interface to SNAP nn Cu potential
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# Initialize simulation
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variable nsteps index 100
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variable nrep equal 4
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variable a equal 3.621262
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units metal
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# generate the box and atom positions using a FCC lattice
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variable nx equal ${nrep}
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variable ny equal ${nrep}
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variable nz equal ${nrep}
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boundary p p p
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lattice fcc $a
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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create_box 1 box
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create_atoms 1 box
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mass 1 63.546
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# choose potential
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pair_style mliap model nn Cu.nn.mliap.model descriptor sna Cu.snap.mliap.descriptor
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pair_coeff * * Cu
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# Setup output
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compute eatom all pe/atom
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compute energy all reduce sum c_eatom
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compute satom all stress/atom NULL
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compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
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variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
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thermo_style custom step temp epair c_energy etotal press v_press
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thermo 10
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thermo_modify norm yes
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# Set up NVE run
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timestep 0.5e-3
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neighbor 1.0 bin
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neigh_modify once no every 1 delay 0 check yes
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# Run MD
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velocity all create 300.0 4928459 loop geom
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fix 1 all nve
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run ${nsteps}
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53
examples/mliap/in.mliap.nn.Ta06A
Normal file
53
examples/mliap/in.mliap.nn.Ta06A
Normal file
@ -0,0 +1,53 @@
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# Demonstrate MLIAP interface to linear SNAP potential
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# Initialize simulation
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variable nsteps index 100
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variable nrep equal 4
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variable a equal 3.316
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable ny equal ${nrep}
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variable nz equal ${nrep}
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boundary p p p
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lattice bcc $a
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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create_box 1 box
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create_atoms 1 box
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mass 1 180.88
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# choose potential
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include Ta06A.nn.mliap
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# Setup output
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compute eatom all pe/atom
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compute energy all reduce sum c_eatom
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compute satom all stress/atom NULL
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compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
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variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
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thermo_style custom step temp epair c_energy etotal press v_press
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thermo 10
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thermo_modify norm yes
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# Set up NVE run
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timestep 0.5e-3
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neighbor 1.0 bin
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neigh_modify once no every 1 delay 0 check yes
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# Run MD
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velocity all create 300.0 4928459 loop geom
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fix 1 all nve
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run ${nsteps}
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@ -24,7 +24,7 @@ mass 1 180.88
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# choose potential
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include Ta06A.mliap.pytorch
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include Ta06A.pytorch.mliap
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# Setup output
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134
examples/mliap/log.03Mar21.mliap.nn.Cu.g++.1
Normal file
134
examples/mliap/log.03Mar21.mliap.nn.Cu.g++.1
Normal file
@ -0,0 +1,134 @@
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LAMMPS (10 Feb 2021)
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using 1 OpenMP thread(s) per MPI task
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# Demonstrate MLIAP interface to SNAP nn Cu potential
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# Initialize simulation
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variable nsteps index 100
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variable nrep equal 4
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variable a equal 3.621262
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units metal
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# generate the box and atom positions using a FCC lattice
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variable nx equal ${nrep}
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variable nx equal 4
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variable ny equal ${nrep}
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variable ny equal 4
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variable nz equal ${nrep}
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variable nz equal 4
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boundary p p p
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lattice fcc $a
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lattice fcc 3.621262
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Lattice spacing in x,y,z = 3.6212620 3.6212620 3.6212620
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 4 0 ${ny} 0 ${nz}
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region box block 0 4 0 4 0 ${nz}
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region box block 0 4 0 4 0 4
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create_box 1 box
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.485048 14.485048 14.485048)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 256 atoms
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create_atoms CPU = 0.000 seconds
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mass 1 63.546
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# choose potential
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pair_style mliap model nn Cu.nn.mliap.model descriptor sna Cu.snap.mliap.descriptor
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Reading potential file Cu.nn.mliap.model with DATE: 2021-03-03
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Reading potential file Cu.snap.mliap.descriptor with DATE: 2021-03-03
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SNAP keyword rcutfac 5.0
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SNAP keyword twojmax 6
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SNAP keyword nelems 1
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SNAP keyword elems Cu
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SNAP keyword radelems 0.5
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SNAP keyword welems 1.0
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SNAP keyword rfac0 0.99363
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SNAP keyword rmin0 0
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SNAP keyword bzeroflag 0
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SNAP keyword switchflag 1
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pair_coeff * * Cu
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# Setup output
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compute eatom all pe/atom
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compute energy all reduce sum c_eatom
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compute satom all stress/atom NULL
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compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
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variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
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thermo_style custom step temp epair c_energy etotal press v_press
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thermo 10
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thermo_modify norm yes
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# Set up NVE run
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timestep 0.5e-3
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neighbor 1.0 bin
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neigh_modify once no every 1 delay 0 check yes
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# Run MD
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velocity all create 300.0 4928459 loop geom
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fix 1 all nve
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run ${nsteps}
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run 100
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 6
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ghost atom cutoff = 6
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binsize = 3, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair mliap, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 31.17 | 31.17 | 31.17 Mbytes
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Step Temp E_pair c_energy TotEng Press v_press
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0 300 -4.0935581 -4.0935581 -4.0549315 -2916.7505 2916.7505
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10 294.19698 -4.0927997 -4.0927997 -4.0549203 -2653.7504 2653.7504
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20 277.15991 -4.0905816 -4.0905816 -4.0548958 -1875.7718 1875.7718
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30 250.30462 -4.0870777 -4.0870777 -4.0548496 -618.45378 618.45378
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40 215.94455 -4.0825861 -4.0825861 -4.0547821 1014.6151 -1014.6151
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50 177.29307 -4.0775299 -4.0775299 -4.0547025 2846.7675 -2846.7675
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60 138.26899 -4.072429 -4.072429 -4.0546261 4698.9654 -4698.9654
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70 103.04321 -4.0678341 -4.0678341 -4.0545667 6401.8077 -6401.8077
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80 75.426905 -4.0642423 -4.0642423 -4.0545307 7766.2217 -7766.2217
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90 58.150738 -4.0620015 -4.0620015 -4.0545143 8668.0598 -8668.0598
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100 52.301012 -4.0612408 -4.0612408 -4.0545067 9049.3141 -9049.3141
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Loop time of 12.7584 on 1 procs for 100 steps with 256 atoms
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Performance: 0.339 ns/day, 70.880 hours/ns, 7.838 timesteps/s
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100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 12.755 | 12.755 | 12.755 | 0.0 | 99.97
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0014069 | 0.0014069 | 0.0014069 | 0.0 | 0.01
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Output | 0.00085897 | 0.00085897 | 0.00085897 | 0.0 | 0.01
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Modify | 0.00075486 | 0.00075486 | 0.00075486 | 0.0 | 0.01
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Other | | 0.0003242 | | | 0.00
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Nlocal: 256.000 ave 256 max 256 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1431.00 ave 1431 max 1431 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 ave 0 max 0 min
|
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 19968.0 ave 19968 max 19968 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 19968
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Ave neighs/atom = 78.000000
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:12
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134
examples/mliap/log.03Mar21.mliap.nn.Cu.g++.4
Normal file
134
examples/mliap/log.03Mar21.mliap.nn.Cu.g++.4
Normal file
@ -0,0 +1,134 @@
|
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LAMMPS (10 Feb 2021)
|
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using 1 OpenMP thread(s) per MPI task
|
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# Demonstrate MLIAP interface to SNAP nn Cu potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.621262
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a FCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
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variable nz equal ${nrep}
|
||||
variable nz equal 4
|
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|
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boundary p p p
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|
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lattice fcc $a
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lattice fcc 3.621262
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Lattice spacing in x,y,z = 3.6212620 3.6212620 3.6212620
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
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region box block 0 4 0 ${ny} 0 ${nz}
|
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region box block 0 4 0 4 0 ${nz}
|
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region box block 0 4 0 4 0 4
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create_box 1 box
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.485048 14.485048 14.485048)
|
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
|
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Created 256 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 63.546
|
||||
|
||||
# choose potential
|
||||
|
||||
pair_style mliap model nn Cu.nn.mliap.model descriptor sna Cu.snap.mliap.descriptor
|
||||
Reading potential file Cu.nn.mliap.model with DATE: 2021-03-03
|
||||
Reading potential file Cu.snap.mliap.descriptor with DATE: 2021-03-03
|
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SNAP keyword rcutfac 5.0
|
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SNAP keyword twojmax 6
|
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SNAP keyword nelems 1
|
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SNAP keyword elems Cu
|
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SNAP keyword radelems 0.5
|
||||
SNAP keyword welems 1.0
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword switchflag 1
|
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pair_coeff * * Cu
|
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|
||||
# Setup output
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp epair c_energy etotal press v_press
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
|
||||
timestep 0.5e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6
|
||||
ghost atom cutoff = 6
|
||||
binsize = 3, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair mliap, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 30.85 | 30.85 | 30.85 Mbytes
|
||||
Step Temp E_pair c_energy TotEng Press v_press
|
||||
0 300 -4.0935581 -4.0935581 -4.0549315 -2916.7505 2916.7505
|
||||
10 294.19698 -4.0927997 -4.0927997 -4.0549203 -2653.7504 2653.7504
|
||||
20 277.15991 -4.0905816 -4.0905816 -4.0548958 -1875.7718 1875.7718
|
||||
30 250.30462 -4.0870777 -4.0870777 -4.0548496 -618.45378 618.45378
|
||||
40 215.94455 -4.0825861 -4.0825861 -4.0547821 1014.6151 -1014.6151
|
||||
50 177.29307 -4.0775299 -4.0775299 -4.0547025 2846.7675 -2846.7675
|
||||
60 138.26899 -4.072429 -4.072429 -4.0546261 4698.9654 -4698.9654
|
||||
70 103.04321 -4.0678341 -4.0678341 -4.0545667 6401.8077 -6401.8077
|
||||
80 75.426905 -4.0642423 -4.0642423 -4.0545307 7766.2217 -7766.2217
|
||||
90 58.150738 -4.0620015 -4.0620015 -4.0545143 8668.0598 -8668.0598
|
||||
100 52.301012 -4.0612408 -4.0612408 -4.0545067 9049.3141 -9049.3141
|
||||
Loop time of 3.22769 on 4 procs for 100 steps with 256 atoms
|
||||
|
||||
Performance: 1.338 ns/day, 17.932 hours/ns, 30.982 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.19 | 3.2037 | 3.2196 | 0.7 | 99.26
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0061415 | 0.022081 | 0.035855 | 8.9 | 0.68
|
||||
Output | 0.00093221 | 0.00094824 | 0.00098861 | 0.0 | 0.03
|
||||
Modify | 0.0002173 | 0.00022773 | 0.00024477 | 0.0 | 0.01
|
||||
Other | | 0.0006805 | | | 0.02
|
||||
|
||||
Nlocal: 64.0000 ave 64 max 64 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 843.000 ave 843 max 843 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4992.00 ave 4992 max 4992 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19968
|
||||
Ave neighs/atom = 78.000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
157
examples/mliap/log.03Mar21.mliap.nn.Ta06A.g++.1
Normal file
157
examples/mliap/log.03Mar21.mliap.nn.Ta06A.g++.1
Normal file
@ -0,0 +1,157 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate MLIAP interface to linear SNAP potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.316
|
||||
Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000 13.264000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
# choose potential
|
||||
|
||||
include Ta06A.nn.mliap
|
||||
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# Definition of SNAP potential Ta_Cand06A
|
||||
# Assumes 1 LAMMPS atom type
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
|
||||
# Specify hybrid with SNAP, ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 4.8 mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor
|
||||
Reading potential file Ta06A.nn.mliap.model with DATE: 2021-03-03
|
||||
Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
|
||||
SNAP keyword rcutfac 4.67637
|
||||
SNAP keyword twojmax 6
|
||||
SNAP keyword nelems 1
|
||||
SNAP keyword elems Ta
|
||||
SNAP keyword radelems 0.5
|
||||
SNAP keyword welems 1
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff 1 1 zbl 73 ${zblz}
|
||||
pair_coeff 1 1 zbl 73 73
|
||||
pair_coeff * * mliap Ta
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp epair c_energy etotal press v_press
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
|
||||
timestep 0.5e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.8
|
||||
ghost atom cutoff = 5.8
|
||||
binsize = 2.9, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair zbl, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair mliap, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.15 | 18.15 | 18.15 Mbytes
|
||||
Step Temp E_pair c_energy TotEng Press v_press
|
||||
0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661
|
||||
10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796
|
||||
20 284.53666 -11.849587 -11.849587 -11.813095 2289.1527 -2289.1527
|
||||
30 266.51577 -11.847275 -11.847275 -11.813095 1851.7131 -1851.7131
|
||||
40 243.05007 -11.844266 -11.844266 -11.813095 1570.684 -1570.684
|
||||
50 215.51032 -11.840734 -11.840734 -11.813094 1468.1899 -1468.1899
|
||||
60 185.48331 -11.836883 -11.836883 -11.813094 1524.8757 -1524.8757
|
||||
70 154.6736 -11.832931 -11.832931 -11.813094 1698.3351 -1698.3351
|
||||
80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715
|
||||
90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563
|
||||
100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526
|
||||
Loop time of 3.05207 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 1.415 ns/day, 16.956 hours/ns, 32.765 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.0503 | 3.0503 | 3.0503 | 0.0 | 99.94
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00072395 | 0.00072395 | 0.00072395 | 0.0 | 0.02
|
||||
Output | 0.00050893 | 0.00050893 | 0.00050893 | 0.0 | 0.02
|
||||
Modify | 0.00037375 | 0.00037375 | 0.00037375 | 0.0 | 0.01
|
||||
Other | | 0.0001878 | | | 0.01
|
||||
|
||||
Nlocal: 128.000 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 727.000 ave 727 max 727 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3712.00 ave 3712 max 3712 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 7424.00 ave 7424 max 7424 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7424
|
||||
Ave neighs/atom = 58.000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:03
|
||||
157
examples/mliap/log.03Mar21.mliap.nn.Ta06A.g++.4
Normal file
157
examples/mliap/log.03Mar21.mliap.nn.Ta06A.g++.4
Normal file
@ -0,0 +1,157 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate MLIAP interface to linear SNAP potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.316
|
||||
Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000 13.264000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
# choose potential
|
||||
|
||||
include Ta06A.nn.mliap
|
||||
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# Definition of SNAP potential Ta_Cand06A
|
||||
# Assumes 1 LAMMPS atom type
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
|
||||
# Specify hybrid with SNAP, ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 4.8 mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor
|
||||
Reading potential file Ta06A.nn.mliap.model with DATE: 2021-03-03
|
||||
Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
|
||||
SNAP keyword rcutfac 4.67637
|
||||
SNAP keyword twojmax 6
|
||||
SNAP keyword nelems 1
|
||||
SNAP keyword elems Ta
|
||||
SNAP keyword radelems 0.5
|
||||
SNAP keyword welems 1
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff 1 1 zbl 73 ${zblz}
|
||||
pair_coeff 1 1 zbl 73 73
|
||||
pair_coeff * * mliap Ta
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp epair c_energy etotal press v_press
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
|
||||
timestep 0.5e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.8
|
||||
ghost atom cutoff = 5.8
|
||||
binsize = 2.9, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair zbl, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair mliap, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.06 | 18.06 | 18.06 Mbytes
|
||||
Step Temp E_pair c_energy TotEng Press v_press
|
||||
0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661
|
||||
10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796
|
||||
20 284.53666 -11.849587 -11.849587 -11.813095 2289.1527 -2289.1527
|
||||
30 266.51577 -11.847275 -11.847275 -11.813095 1851.7131 -1851.7131
|
||||
40 243.05007 -11.844266 -11.844266 -11.813095 1570.684 -1570.684
|
||||
50 215.51032 -11.840734 -11.840734 -11.813094 1468.1899 -1468.1899
|
||||
60 185.48331 -11.836883 -11.836883 -11.813094 1524.8757 -1524.8757
|
||||
70 154.6736 -11.832931 -11.832931 -11.813094 1698.3351 -1698.3351
|
||||
80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715
|
||||
90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563
|
||||
100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526
|
||||
Loop time of 0.858301 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 5.033 ns/day, 4.768 hours/ns, 116.509 timesteps/s
|
||||
100.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.75351 | 0.79999 | 0.85429 | 4.2 | 93.21
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0026857 | 0.057019 | 0.10354 | 15.8 | 6.64
|
||||
Output | 0.00078796 | 0.00080864 | 0.00085671 | 0.0 | 0.09
|
||||
Modify | 0.00011437 | 0.00012275 | 0.00013339 | 0.0 | 0.01
|
||||
Other | | 0.0003564 | | | 0.04
|
||||
|
||||
Nlocal: 32.0000 ave 32 max 32 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 431.000 ave 431 max 431 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 928.000 ave 928 max 928 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1856.00 ave 1856 max 1856 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7424
|
||||
Ave neighs/atom = 58.000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,5 +1,5 @@
|
||||
LAMMPS (30 Nov 2020)
|
||||
using 48 OpenMP thread(s) per MPI task
|
||||
LAMMPS (10 Feb 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate MLIAP/PyTorch interface to linear SNAP potential
|
||||
|
||||
# Initialize simulation
|
||||
@ -32,13 +32,13 @@ Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
create_atoms CPU = 0.002 seconds
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
# choose potential
|
||||
|
||||
include Ta06A.mliap.pytorch
|
||||
include Ta06A.pytorch.mliap
|
||||
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# Definition of SNAP potential Ta_Cand06A
|
||||
@ -50,9 +50,9 @@ variable zblz equal 73
|
||||
|
||||
# Specify hybrid with SNAP, ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pkl descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pkl descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 4.8 mliap model mliappy Ta06A.mliap.pytorch.model.pkl descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 4.8 mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
|
||||
Loading python model complete.
|
||||
Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
|
||||
SNAP keyword rcutfac 4.67637
|
||||
@ -112,7 +112,7 @@ Neighbor list info ...
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 159.8 | 159.8 | 159.8 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.15 | 18.15 | 18.15 Mbytes
|
||||
Step Temp E_pair c_energy TotEng Press v_press
|
||||
0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661
|
||||
10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796
|
||||
@ -125,20 +125,20 @@ Step Temp E_pair c_energy TotEng Press v_press
|
||||
80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715
|
||||
90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563
|
||||
100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526
|
||||
Loop time of 2.00236 on 48 procs for 100 steps with 128 atoms
|
||||
Loop time of 2.0472 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 2.157 ns/day, 11.124 hours/ns, 49.941 timesteps/s
|
||||
288.8% CPU use with 1 MPI tasks x 48 OpenMP threads
|
||||
Performance: 2.110 ns/day, 11.373 hours/ns, 48.847 timesteps/s
|
||||
100.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.9998 | 1.9998 | 1.9998 | 0.0 | 99.87
|
||||
Pair | 2.0443 | 2.0443 | 2.0443 | 0.0 | 99.86
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0011814 | 0.0011814 | 0.0011814 | 0.0 | 0.06
|
||||
Output | 0.00059724 | 0.00059724 | 0.00059724 | 0.0 | 0.03
|
||||
Modify | 0.00047352 | 0.00047352 | 0.00047352 | 0.0 | 0.02
|
||||
Other | | 0.0003468 | | | 0.02
|
||||
Comm | 0.001157 | 0.001157 | 0.001157 | 0.0 | 0.06
|
||||
Output | 0.00080857 | 0.00080857 | 0.00080857 | 0.0 | 0.04
|
||||
Modify | 0.00053188 | 0.00053188 | 0.00053188 | 0.0 | 0.03
|
||||
Other | | 0.0004304 | | | 0.02
|
||||
|
||||
Nlocal: 128.000 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
LAMMPS (30 Nov 2020)
|
||||
using 48 OpenMP thread(s) per MPI task
|
||||
LAMMPS (10 Feb 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate MLIAP/PyTorch interface to linear SNAP potential
|
||||
|
||||
# Initialize simulation
|
||||
@ -32,13 +32,13 @@ Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
create_atoms CPU = 0.002 seconds
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
# choose potential
|
||||
|
||||
include Ta06A.mliap.pytorch
|
||||
include Ta06A.pytorch.mliap
|
||||
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# Definition of SNAP potential Ta_Cand06A
|
||||
@ -50,9 +50,9 @@ variable zblz equal 73
|
||||
|
||||
# Specify hybrid with SNAP, ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pkl descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pkl descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 4.8 mliap model mliappy Ta06A.mliap.pytorch.model.pkl descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 4.8 mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
|
||||
Loading python model complete.
|
||||
Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
|
||||
SNAP keyword rcutfac 4.67637
|
||||
@ -112,7 +112,7 @@ Neighbor list info ...
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 159.7 | 159.7 | 159.7 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.06 | 18.06 | 18.06 Mbytes
|
||||
Step Temp E_pair c_energy TotEng Press v_press
|
||||
0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661
|
||||
10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796
|
||||
@ -125,20 +125,20 @@ Step Temp E_pair c_energy TotEng Press v_press
|
||||
80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715
|
||||
90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563
|
||||
100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526
|
||||
Loop time of 0.562802 on 192 procs for 100 steps with 128 atoms
|
||||
Loop time of 0.572344 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 7.676 ns/day, 3.127 hours/ns, 177.682 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x 48 OpenMP threads
|
||||
Performance: 7.548 ns/day, 3.180 hours/ns, 174.720 timesteps/s
|
||||
100.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.53583 | 0.54622 | 0.55401 | 0.9 | 97.05
|
||||
Pair | 0.51796 | 0.5401 | 0.56608 | 2.4 | 94.37
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0071442 | 0.01491 | 0.025289 | 5.4 | 2.65
|
||||
Output | 0.00092525 | 0.00095771 | 0.0010166 | 0.0 | 0.17
|
||||
Modify | 0.00014479 | 0.00015043 | 0.00015893 | 0.0 | 0.03
|
||||
Other | | 0.0005624 | | | 0.10
|
||||
Comm | 0.0044844 | 0.030393 | 0.052464 | 10.2 | 5.31
|
||||
Output | 0.001 | 0.0010351 | 0.0011083 | 0.1 | 0.18
|
||||
Modify | 0.0001468 | 0.00016417 | 0.00017977 | 0.0 | 0.03
|
||||
Other | | 0.0006567 | | | 0.11
|
||||
|
||||
Nlocal: 32.0000 ave 32 max 32 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
@ -154,4 +154,4 @@ Ave neighs/atom = 58.000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:02
|
||||
Total wall time: 0:00:05
|
||||
|
||||
@ -1,154 +0,0 @@
|
||||
LAMMPS (19 Mar 2020)
|
||||
# Demonstrate SNAP Ta potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.316
|
||||
Lattice spacing in x,y,z = 3.316 3.316 3.316
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
create_atoms CPU = 0.000254 secs
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
# choose potential
|
||||
|
||||
include Ta06A.snap
|
||||
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# Definition of SNAP potential Ta_Cand06A
|
||||
# Assumes 1 LAMMPS atom type
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
|
||||
# Specify hybrid with SNAP, ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
|
||||
pair_style hybrid/overlay zbl 4 4.8 snap
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff 1 1 zbl 73 ${zblz}
|
||||
pair_coeff 1 1 zbl 73 73
|
||||
pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
|
||||
Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
|
||||
SNAP Element = Ta, Radius 0.5, Weight 1
|
||||
Reading potential file Ta06A.snapparam with DATE: 2014-09-05
|
||||
SNAP keyword rcutfac 4.67637
|
||||
SNAP keyword twojmax 6
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword quadraticflag 0
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp epair c_energy etotal press v_press
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
|
||||
timestep 0.5e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.8
|
||||
ghost atom cutoff = 5.8
|
||||
binsize = 2.9, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair zbl, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair snap, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.591 | 6.591 | 6.591 Mbytes
|
||||
Step Temp E_pair c_energy TotEng Press v_press
|
||||
0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661
|
||||
10 295.96579 -11.851053 -11.851053 -11.813095 2696.1559 -2696.1559
|
||||
20 284.32535 -11.84956 -11.84956 -11.813095 2301.3713 -2301.3713
|
||||
30 266.04602 -11.847215 -11.847215 -11.813095 1832.1745 -1832.1745
|
||||
40 242.2862 -11.844168 -11.844168 -11.813095 1492.6765 -1492.6765
|
||||
50 214.48968 -11.840603 -11.840603 -11.813094 1312.8908 -1312.8908
|
||||
60 184.32523 -11.836734 -11.836734 -11.813094 1284.582 -1284.582
|
||||
70 153.58055 -11.832791 -11.832791 -11.813094 1374.4457 -1374.4457
|
||||
80 124.04276 -11.829003 -11.829003 -11.813094 1537.703 -1537.703
|
||||
90 97.37622 -11.825582 -11.825582 -11.813094 1734.9662 -1734.9662
|
||||
100 75.007873 -11.822714 -11.822714 -11.813094 1930.8005 -1930.8005
|
||||
Loop time of 0.995328 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 4.340 ns/day, 5.530 hours/ns, 100.469 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.99426 | 0.99426 | 0.99426 | 0.0 | 99.89
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.000305 | 0.000305 | 0.000305 | 0.0 | 0.03
|
||||
Output | 0.000413 | 0.000413 | 0.000413 | 0.0 | 0.04
|
||||
Modify | 0.000159 | 0.000159 | 0.000159 | 0.0 | 0.02
|
||||
Other | | 0.000191 | | | 0.02
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 727 ave 727 max 727 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3712 ave 3712 max 3712 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 7424 ave 7424 max 7424 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7424
|
||||
Ave neighs/atom = 58
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:01
|
||||
41
potentials/Cu.nn.mliap.model
Normal file
41
potentials/Cu.nn.mliap.model
Normal file
@ -0,0 +1,41 @@
|
||||
# DATE: 2021-03-03 UNITS: metal CONTRIBUTOR: Pedro Antonio Santos Florez pedroantoniosantosf@gmail.com CITATION: none
|
||||
# Neural networks weights generated in PyXtal_FF
|
||||
|
||||
# total_species nparams
|
||||
1 71
|
||||
|
||||
# NET ndescriptors nlayers activation_func for layer 1, number of nodes for layer 1, ..., ..., ....,
|
||||
NET 30 3 tanh 2 tanh 2 linear 1
|
||||
|
||||
# Scale0
|
||||
98.5564567301067 0.1817576370006 -5.0513436999162 0.0453581866073 -4.4382278670569
|
||||
-2.6985391112026 -4.9445068940273 7.8840372041149 -12.8729456412560 -2.9748781222888
|
||||
-1.7702149043285 -4.6911979511282 -1.8167140506334 67.7067032503211 -12.5675074252146
|
||||
-10.3889411514447 -2.6194029974308 1.8750503488944 -5.0934919399232 4.2037760919263
|
||||
20.6488797181668 -8.2381178902428 -3.1311436510232 -1.1570117080256 2.1652328079269
|
||||
0.0854872341687 73.5970916724043 -5.3230176040510 -5.3409170596296 -6.4491186818574
|
||||
|
||||
# Scale1
|
||||
783.0204659783215 33.6453931227955 7.9068346594951 32.2509031640463 5.6624925894670
|
||||
5.6511565657016 8.2175114613285 108.9434600935519 16.3162547782998 6.4485086884047
|
||||
9.5767453287024 24.1576638495153 25.1723098340896 202.6741688060115 26.3843102888906
|
||||
19.7937707236334 13.9016635198379 14.1399097533048 72.7078614093291 39.8358080634714
|
||||
370.1745750951991 21.6864533954642 14.6554778261065 18.6456437491491 43.2946309680355
|
||||
68.9168418942695 481.9819429675007 14.5585849595560 61.9026061535013 112.5968384702330
|
||||
|
||||
# Coefficients
|
||||
-0.2503221860648 0.4607794046378 0.4080552184108 0.0043328332206 0.2778722163950
|
||||
-0.0050555739235 0.0406748042003 -0.1188215011883 0.4669700426246 0.4050949681583
|
||||
0.3004118858813 -0.3937378155782 0.5165632847373 0.1381866719908 -0.3996533578004
|
||||
0.1330571447244 0.1124773980921 0.1548275555377 -0.6221152970188 -0.7813275942231
|
||||
-0.4320969824072 0.2045533448767 -0.1687644566507 -0.0424066840175 -0.1981208883936
|
||||
-0.3406471991751 0.1272788573915 -0.1236220514264 0.6482374783971 -0.0590428211363
|
||||
0.1326060235944 0.1890472518561 -0.5428894028577 0.0229420637813 0.0750842032804
|
||||
-0.2443049940974 0.5265826743321 -0.1802773940492 0.0309737044359 -0.4987806786020
|
||||
-0.6233577810656 -0.9910225261357 0.3430680860751 0.2918559145139 0.0666915892882
|
||||
-0.2558026088950 0.0417769401952 -0.2582828540822 -0.3685977011673 0.4793473883461
|
||||
1.0290706767456 0.0400544448686 -0.1474888333296 0.2403156153173 0.1050109023846
|
||||
0.1413378531949 0.0907250056918 -0.1185878739508 0.1471942864979 -0.2829701766758
|
||||
0.1137318187684 0.0476123438306 0.8040349098084 -0.5432518550512 0.2312003570779
|
||||
0.6886872913686 -0.1247049894693 0.6848986783339 -2.6353147047309 -0.7173579584864
|
||||
-1.0543148168289
|
||||
21
potentials/Cu.snap.mliap.descriptor
Normal file
21
potentials/Cu.snap.mliap.descriptor
Normal file
@ -0,0 +1,21 @@
|
||||
# DATE: 2021-03-03 UNITS: metal CONTRIBUTOR: Pedro Antonio Santos Florez pedroantoniosantosf@gmail.com CITATION: none
|
||||
|
||||
# LAMMPS SNAP parameters for Cu
|
||||
|
||||
# required
|
||||
rcutfac 5.0
|
||||
twojmax 6
|
||||
|
||||
# elements
|
||||
|
||||
nelems 1
|
||||
elems Cu
|
||||
radelems 0.5
|
||||
welems 1.0
|
||||
|
||||
# optional
|
||||
|
||||
rfac0 0.99363
|
||||
rmin0 0
|
||||
bzeroflag 0
|
||||
switchflag 1
|
||||
@ -100,6 +100,9 @@ meam.spline modified EAM (MEAM) spline potential
|
||||
meam.sw.spline modified EAM (MEAM) Stillinger-Weber spline potential
|
||||
mesocnt mesoscopic carbon nanotube (CNT) potential
|
||||
mgpt model generalized pseudopotential theory (MGPT) potential
|
||||
mliap MLIAP potential
|
||||
mliap.descriptor MLIAP potential descriptor
|
||||
mliap.model MLIAP potential model
|
||||
nb3b.harmonic nonbonded 3-body harmonic potential
|
||||
poly polymorphic 3-body potential
|
||||
reax ReaxFF potential (see README.reax for more info)
|
||||
|
||||
18
potentials/Ta06A.nn.mliap
Normal file
18
potentials/Ta06A.nn.mliap
Normal file
@ -0,0 +1,18 @@
|
||||
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# Definition of SNAP potential Ta_Cand06A
|
||||
# Assumes 1 LAMMPS atom type
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
|
||||
# Specify hybrid with SNAP, ZBL
|
||||
|
||||
pair_style hybrid/overlay &
|
||||
zbl ${zblcutinner} ${zblcutouter} &
|
||||
mliap model nn Ta06A.nn.mliap.model &
|
||||
descriptor sna Ta06A.mliap.descriptor
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff * * mliap Ta
|
||||
|
||||
15
potentials/Ta06A.nn.mliap.model
Normal file
15
potentials/Ta06A.nn.mliap.model
Normal file
@ -0,0 +1,15 @@
|
||||
# DATE: 2021-03-03 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# LAMMPS SNAP_nn coefficients for Ta_Cand06A
|
||||
|
||||
# nelements nparams
|
||||
1 31
|
||||
# NET #ndescriptors #nlayers #activation_func for layer 1 #number of nodes for layer 1, ..., ..., ....,
|
||||
NET 30 1 linear 1
|
||||
#scale0
|
||||
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
#scale1
|
||||
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
|
||||
#coeff
|
||||
-2.92477
|
||||
-0.01137 -0.00775 -0.04907 -0.15047 0.09157 0.05590 0.05785 -0.11615 -0.17122 -0.10583 0.03941 -0.11284 0.03939 -0.07331 -0.06582 -0.09341 -0.10587 -0.15497 0.04820 0.00205 0.00060 -0.04898 -0.05084 -0.03371 -0.01441 -0.01501 -0.00599 -0.06373 0.03965 0.01072
|
||||
@ -1,57 +0,0 @@
|
||||
This package provides a general interface to families of
|
||||
machine-learning interatomic potentials (MLIAPs). This interface consists
|
||||
of a mliap pair style and a mliap compute.
|
||||
|
||||
The mliap pair style is used when running simulations with energies and
|
||||
forces calculated by an MLIAP. The interface allows separate
|
||||
definitions of the interatomic potential functional form (*model*)
|
||||
and the geometric quantities that characterize the atomic positions
|
||||
(*descriptor*). By defining *model* and *descriptor* separately,
|
||||
it is possible to use many different models with a given descriptor,
|
||||
or many different descriptors with a given model. The pair_style
|
||||
supports the following models: *linear*, *quadratic*, and
|
||||
*mliappy* (general Python interface to things like PyTorch, see below
|
||||
for build instructions).
|
||||
It currently supports only one class of descriptors,
|
||||
*sna*, the SNAP descriptors, including the
|
||||
linear, quadratic, and chem variants.
|
||||
It is straightforward to add new descriptor and model
|
||||
styles.
|
||||
|
||||
The mliap compute style provides gradients of the energy, force,
|
||||
and stress tensor w.r.t. model parameters.
|
||||
These are useful when training MLIAPs to match target data.
|
||||
Any *model or *descriptor* that has been implemented for the
|
||||
*mliap* pair style can also be accessed by the *mliap* compute.
|
||||
In addition to the energy, force, and stress gradients, w.r.t.
|
||||
each *model* parameter, the compute also calculates the energy,
|
||||
force, and stress contributions from a user-specified
|
||||
reference potential.
|
||||
|
||||
To see how this command
|
||||
can be used within a Python workflow to train machine-learning interatomic
|
||||
potentials, see the examples in FitSNAP https://github.com/FitSNAP/FitSNAP.
|
||||
|
||||
*Additional instructions for building MLIAP with Python support enabled*
|
||||
|
||||
The *mliappy* energy model requires that the MLIAP package
|
||||
be compiled with Python support enabled.
|
||||
This extension, written by Nick Lubbers (LANL),
|
||||
provides a coupling to PyTorch and other Python modules.
|
||||
This should be automatically
|
||||
enabled by default if the prerequisite software is installed. It can be
|
||||
enforced during CMake configuration by setting the variable
|
||||
MLIAP_ENABLE_PYTHON=yes or for conventional build by adding -DMLIAP_PYTHON
|
||||
to the LMP_INC variable in your makefile and running the cythonize script
|
||||
on the .pyx file(s) copied to the src folder.
|
||||
|
||||
This requires to also install the PYTHON package and have the cython
|
||||
(https://cython.org) software installed. During configuration/compilation
|
||||
the cythonize script will be used to convert the provided .pyx file(s)
|
||||
to C++ code. Please do not run the cythonize script in the src/MLIAP folder.
|
||||
If you have done so by accident, you need to delete the generated .cpp and .h
|
||||
file(s) in the src/MLIAP folder or there may be problems during compilation.
|
||||
|
||||
More information on building LAMMPS with this package is here:
|
||||
|
||||
https://lammps.sandia.gov/doc/Build_extras.html#mliap
|
||||
41
src/MLIAP/README.md
Normal file
41
src/MLIAP/README.md
Normal file
@ -0,0 +1,41 @@
|
||||
This package provides a general interface to families of machine-learning interatomic potentials (MLIAPs).
|
||||
This interface consists of a `mliap pair style` and a `mliap compute`.
|
||||
The `mliap pair style` is used when running simulations with energies and
|
||||
forces calculated by an MLIAP. The interface allows separate
|
||||
definitions of the interatomic potential functional form (`model`)
|
||||
and the geometric quantities that characterize the atomic positions
|
||||
(`descriptor`). By defining `model` and `descriptor` separately,
|
||||
it is possible to use many different models with a given descriptor,
|
||||
or many different descriptors with a given model. The pair_style
|
||||
supports the following models:
|
||||
|
||||
- `linear`,
|
||||
- `quadratic`,
|
||||
- `nn` (neural networks)
|
||||
- `mliappy` (general Python interface to things like PyTorch).
|
||||
|
||||
It currently supports only one class of descriptors, `sna`, the SNAP descriptors.
|
||||
It is straightforward to add new descriptor and model styles.
|
||||
|
||||
The `mliap compute` style provides gradients of the energy, force,
|
||||
and stress tensor w.r.t. model parameters.
|
||||
These are useful when training MLIAPs to match target data.
|
||||
Any `model` or `descriptor` that has been implemented for the
|
||||
`mliap` pair style can also be accessed by the `mliap` compute.
|
||||
In addition to the energy, force, and stress gradients, w.r.t.
|
||||
each `model` parameter, the compute also calculates the energy,
|
||||
force, and stress contributions from a user-specified
|
||||
reference potential.
|
||||
|
||||
## Generating the model files from the third-party packages
|
||||
- To train the `linear` and `quadratic` models with the SNAP descriptors, see the examples in [FitSNAP](https://github.com/FitSNAP/FitSNAP).
|
||||
- To train the `nn` model with the SNAP descriptors, check the examples in [PyXtal\_FF](https://github.com/qzhu2017/PyXtal_FF).
|
||||
|
||||
## Building MLIAP with Python support
|
||||
|
||||
The `mliappy` energy model requires that the MLIAP package be compiled with Python support enabled. This extension, written by Nick Lubbers (LANL), provides a coupling to PyTorch and other Python modules. This should be automatically enabled by default if the prerequisite software is installed. It can be enforced during CMake configuration by setting the variable `MLIAP_ENABLE_PYTHON=yes` or for conventional build by adding `-DMLIAP_PYTHON` to the `LMP_INC` variable in your makefile and running the cythonize script on the .pyx file(s) copied to the src folder.
|
||||
|
||||
This requires to also install the PYTHON package and have the [cython](https://cython.org) software installed. During configuration/compilation
|
||||
the cythonize script will be used to convert the provided .pyx file(s) to C++ code. Please do not run the cythonize script in the src/MLIAP folder. If you have done so by accident, you need to delete the generated .cpp and .h file(s) in the src/MLIAP folder or there may be problems during compilation.
|
||||
|
||||
More information on building LAMMPS with this package is [here](https://lammps.sandia.gov/doc/Build_extras.html#mliap).
|
||||
@ -215,7 +215,7 @@ void ComputeMLIAP::init_list(int /*id*/, NeighList *ptr)
|
||||
|
||||
void ComputeMLIAP::compute_array()
|
||||
{
|
||||
int ntotal = atom->nlocal + atom->nghost;
|
||||
int nall = atom->nlocal + atom->nghost;
|
||||
invoked_array = update->ntimestep;
|
||||
|
||||
// clear global array
|
||||
@ -261,7 +261,7 @@ void ComputeMLIAP::compute_array()
|
||||
for (int ielem = 0; ielem < data->nelements; ielem++) {
|
||||
const int elemoffset = data->nparams*ielem;
|
||||
for (int jparam = 0; jparam < data->nparams; jparam++) {
|
||||
for (int i = 0; i < ntotal; i++) {
|
||||
for (int i = 0; i < nall; i++) {
|
||||
double *gradforcei = data->gradforce[i]+elemoffset;
|
||||
tagint irow = 3*(atom->tag[i]-1)+1;
|
||||
mliaparray[irow][jparam+elemoffset] += gradforcei[jparam];
|
||||
@ -307,7 +307,7 @@ void ComputeMLIAP::compute_array()
|
||||
// switch to Voigt notation
|
||||
|
||||
c_virial->compute_vector();
|
||||
irow += 3*data->natoms_array;
|
||||
irow += 3*data->natoms;
|
||||
mliaparrayall[irow++][lastcol] = c_virial->vector[0];
|
||||
mliaparrayall[irow++][lastcol] = c_virial->vector[1];
|
||||
mliaparrayall[irow++][lastcol] = c_virial->vector[2];
|
||||
@ -325,7 +325,7 @@ void ComputeMLIAP::compute_array()
|
||||
void ComputeMLIAP::dbdotr_compute()
|
||||
{
|
||||
double **x = atom->x;
|
||||
int irow0 = 1+data->ndims_force*data->natoms_array;
|
||||
int irow0 = 1+data->ndims_force*data->natoms;
|
||||
|
||||
// sum over bispectrum contributions to forces
|
||||
// on all particles including ghosts
|
||||
|
||||
@ -18,6 +18,7 @@
|
||||
#include "mliap_data.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "error.h"
|
||||
#include "memory.h"
|
||||
#include "mliap_descriptor.h"
|
||||
#include "mliap_model.h"
|
||||
@ -50,12 +51,18 @@ MLIAPData::MLIAPData(LAMMPS *lmp, int gradgradflag_in, int *map_in,
|
||||
ndims_virial = 6;
|
||||
yoffset = nparams*nelements;
|
||||
zoffset = 2*yoffset;
|
||||
natoms_array = atom->natoms;
|
||||
size_array_rows = 1+ndims_force*natoms_array+ndims_virial;
|
||||
natoms = atom->natoms;
|
||||
|
||||
// must check before assigning bigint expression to regular int
|
||||
|
||||
if (1+ndims_force*natoms+ndims_virial > MAXSMALLINT)
|
||||
error->all(FLERR,"Too many atoms for MLIAP package");
|
||||
|
||||
size_array_rows = 1+ndims_force*natoms+ndims_virial;
|
||||
size_array_cols = nparams*nelements+1;
|
||||
size_gradforce = ndims_force*nparams*nelements;
|
||||
|
||||
natoms_max = 0;
|
||||
nlistatoms_max = 0;
|
||||
natomneigh_max = 0;
|
||||
nneigh_max = 0;
|
||||
nmax = 0;
|
||||
@ -102,6 +109,7 @@ void MLIAPData::generate_neighdata(NeighList* list_in, int eflag_in, int vflag_i
|
||||
double **x = atom->x;
|
||||
int *type = atom->type;
|
||||
|
||||
int *ilist = list->ilist;
|
||||
int *numneigh = list->numneigh;
|
||||
int **firstneigh = list->firstneigh;
|
||||
|
||||
@ -115,39 +123,38 @@ void MLIAPData::generate_neighdata(NeighList* list_in, int eflag_in, int vflag_i
|
||||
|
||||
// clear gradforce array
|
||||
|
||||
int ntotal = atom->nlocal + atom->nghost;
|
||||
for (int i = 0; i < ntotal; i++)
|
||||
int nall = atom->nlocal + atom->nghost;
|
||||
for (int i = 0; i < nall; i++)
|
||||
for (int j = 0; j < size_gradforce; j++) {
|
||||
gradforce[i][j] = 0.0;
|
||||
}
|
||||
|
||||
// grow arrays if necessary
|
||||
|
||||
nlistatoms = list->inum;
|
||||
if (nlistatoms_max < nlistatoms) {
|
||||
memory->grow(betas,nlistatoms,ndescriptors,"MLIAPData:betas");
|
||||
memory->grow(descriptors,nlistatoms,ndescriptors,"MLIAPData:descriptors");
|
||||
memory->grow(eatoms,nlistatoms,"MLIAPData:eatoms");
|
||||
nlistatoms_max = nlistatoms;
|
||||
}
|
||||
|
||||
// grow gamma arrays if necessary
|
||||
|
||||
if (gradgradflag == 1) {
|
||||
const int natomgamma = list->inum;
|
||||
if (natomgamma_max < natomgamma) {
|
||||
memory->grow(gamma_row_index,natomgamma,gamma_nnz,"MLIAPData:gamma_row_index");
|
||||
memory->grow(gamma_col_index,natomgamma,gamma_nnz,"MLIAPData:gamma_col_index");
|
||||
memory->grow(gamma,natomgamma,gamma_nnz,"MLIAPData:gamma");
|
||||
natomgamma_max = natomgamma;
|
||||
if (natomgamma_max < nlistatoms) {
|
||||
memory->grow(gamma_row_index,nlistatoms,gamma_nnz,"MLIAPData:gamma_row_index");
|
||||
memory->grow(gamma_col_index,nlistatoms,gamma_nnz,"MLIAPData:gamma_col_index");
|
||||
memory->grow(gamma,nlistatoms,gamma_nnz,"MLIAPData:gamma");
|
||||
natomgamma_max = nlistatoms;
|
||||
}
|
||||
}
|
||||
|
||||
// grow arrays if necessary
|
||||
|
||||
natoms = list->inum;
|
||||
if (natoms_max < natoms) {
|
||||
memory->grow(betas,natoms,ndescriptors,"MLIAPData:betas");
|
||||
memory->grow(descriptors,natoms,ndescriptors,"MLIAPData:descriptors");
|
||||
memory->grow(eatoms,natoms,"MLIAPData:eatoms");
|
||||
natoms_max = natoms;
|
||||
}
|
||||
|
||||
grow_neigharrays();
|
||||
|
||||
int ij = 0;
|
||||
for (int ii = 0; ii < list->inum; ii++) {
|
||||
const int i = list->ilist[ii];
|
||||
for (int ii = 0; ii < nlistatoms; ii++) {
|
||||
const int i = ilist[ii];
|
||||
|
||||
const double xtmp = x[i][0];
|
||||
const double ytmp = x[i][1];
|
||||
@ -197,30 +204,24 @@ void MLIAPData::grow_neigharrays()
|
||||
|
||||
// grow neighbor atom arrays if necessary
|
||||
|
||||
const int natomneigh = list->inum;
|
||||
if (natomneigh_max < natomneigh) {
|
||||
memory->grow(iatoms,natomneigh,"MLIAPData:iatoms");
|
||||
memory->grow(ielems,natomneigh,"MLIAPData:ielems");
|
||||
memory->grow(numneighs,natomneigh,"MLIAPData:numneighs");
|
||||
natomneigh_max = natomneigh;
|
||||
if (natomneigh_max < nlistatoms) {
|
||||
memory->grow(iatoms,nlistatoms,"MLIAPData:iatoms");
|
||||
memory->grow(ielems,nlistatoms,"MLIAPData:ielems");
|
||||
memory->grow(numneighs,nlistatoms,"MLIAPData:numneighs");
|
||||
natomneigh_max = nlistatoms;
|
||||
}
|
||||
|
||||
// grow neighbor arrays if necessary
|
||||
|
||||
int *ilist = list->ilist;
|
||||
int *numneigh = list->numneigh;
|
||||
int **firstneigh = list->firstneigh;
|
||||
|
||||
int iilast = list->inum-1;
|
||||
int ilast = list->ilist[iilast];
|
||||
int upperbound = firstneigh[ilast] - firstneigh[0] + numneigh[ilast];
|
||||
if (nneigh_max >= upperbound) return;
|
||||
|
||||
double **x = atom->x;
|
||||
int *type = atom->type;
|
||||
|
||||
int nneigh = 0;
|
||||
for (int ii = 0; ii < list->inum; ii++) {
|
||||
const int i = list->ilist[ii];
|
||||
for (int ii = 0; ii < nlistatoms; ii++) {
|
||||
const int i = ilist[ii];
|
||||
|
||||
const double xtmp = x[i][0];
|
||||
const double ytmp = x[i][1];
|
||||
@ -272,9 +273,9 @@ double MLIAPData::memory_usage()
|
||||
gamma_nnz*sizeof(double); // gamma
|
||||
}
|
||||
|
||||
bytes += (double)natoms*ndescriptors*sizeof(int); // betas
|
||||
bytes += (double)natoms*ndescriptors*sizeof(int); // descriptors
|
||||
bytes += (double)natoms*sizeof(double); // eatoms
|
||||
bytes += (double)nlistatoms*ndescriptors*sizeof(int); // betas
|
||||
bytes += (double)nlistatoms*ndescriptors*sizeof(int); // descriptors
|
||||
bytes += (double)nlistatoms*sizeof(double); // eatoms
|
||||
|
||||
bytes += (double)natomneigh_max*sizeof(int); // iatoms
|
||||
bytes += (double)natomneigh_max*sizeof(int); // ielems
|
||||
|
||||
@ -30,7 +30,8 @@ class MLIAPData : protected Pointers {
|
||||
double memory_usage();
|
||||
|
||||
int size_array_rows, size_array_cols;
|
||||
int natoms_array, size_gradforce;
|
||||
int natoms;
|
||||
int size_gradforce;
|
||||
int yoffset, zoffset;
|
||||
int ndims_force, ndims_virial;
|
||||
double **gradforce;
|
||||
@ -54,8 +55,8 @@ class MLIAPData : protected Pointers {
|
||||
// data structures for mliap neighbor list
|
||||
// only neighbors strictly inside descriptor cutoff
|
||||
|
||||
int natoms; // current number of atoms
|
||||
int natoms_max; // allocated size of descriptor array
|
||||
int nlistatoms; // current number of atoms in neighborlist
|
||||
int nlistatoms_max; // allocated size of descriptor array
|
||||
int natomneigh_max; // allocated size of atom neighbor arrays
|
||||
int *numneighs; // neighbors count for each atom
|
||||
int *iatoms; // index of each atom
|
||||
|
||||
@ -78,7 +78,7 @@ MLIAPDescriptorSNAP::~MLIAPDescriptorSNAP()
|
||||
void MLIAPDescriptorSNAP::compute_descriptors(class MLIAPData* data)
|
||||
{
|
||||
int ij = 0;
|
||||
for (int ii = 0; ii < data->natoms; ii++) {
|
||||
for (int ii = 0; ii < data->nlistatoms; ii++) {
|
||||
const int ielem = data->ielems[ii];
|
||||
|
||||
// insure rij, inside, wj, and rcutij are of size jnum
|
||||
@ -130,7 +130,7 @@ void MLIAPDescriptorSNAP::compute_forces(class MLIAPData* data)
|
||||
double **f = atom->f;
|
||||
|
||||
int ij = 0;
|
||||
for (int ii = 0; ii < data->natoms; ii++) {
|
||||
for (int ii = 0; ii < data->nlistatoms; ii++) {
|
||||
const int i = data->iatoms[ii];
|
||||
const int ielem = data->ielems[ii];
|
||||
|
||||
@ -204,7 +204,7 @@ void MLIAPDescriptorSNAP::compute_forces(class MLIAPData* data)
|
||||
void MLIAPDescriptorSNAP::compute_force_gradients(class MLIAPData* data)
|
||||
{
|
||||
int ij = 0;
|
||||
for (int ii = 0; ii < data->natoms; ii++) {
|
||||
for (int ii = 0; ii < data->nlistatoms; ii++) {
|
||||
const int i = data->iatoms[ii];
|
||||
const int ielem = data->ielems[ii];
|
||||
|
||||
@ -279,7 +279,7 @@ void MLIAPDescriptorSNAP::compute_force_gradients(class MLIAPData* data)
|
||||
void MLIAPDescriptorSNAP::compute_descriptor_gradients(class MLIAPData* data)
|
||||
{
|
||||
int ij = 0;
|
||||
for (int ii = 0; ii < data->natoms; ii++) {
|
||||
for (int ii = 0; ii < data->nlistatoms; ii++) {
|
||||
const int ielem = data->ielems[ii];
|
||||
|
||||
// insure rij, inside, wj, and rcutij are of size jnum
|
||||
|
||||
@ -57,7 +57,7 @@ void MLIAPModelLinear::compute_gradients(MLIAPData* data)
|
||||
{
|
||||
data->energy = 0.0;
|
||||
|
||||
for (int ii = 0; ii < data->natoms; ii++) {
|
||||
for (int ii = 0; ii < data->nlistatoms; ii++) {
|
||||
const int ielem = data->ielems[ii];
|
||||
|
||||
double* coeffi = coeffelem[ielem];
|
||||
@ -107,7 +107,7 @@ void MLIAPModelLinear::compute_gradgrads(class MLIAPData* data)
|
||||
for (int l = 0; l < data->nelements*data->nparams; l++)
|
||||
data->egradient[l] = 0.0;
|
||||
|
||||
for (int ii = 0; ii < data->natoms; ii++) {
|
||||
for (int ii = 0; ii < data->nlistatoms; ii++) {
|
||||
const int ielem = data->ielems[ii];
|
||||
const int elemoffset = data->nparams*ielem;
|
||||
|
||||
@ -143,7 +143,7 @@ void MLIAPModelLinear::compute_force_gradients(class MLIAPData* data)
|
||||
data->egradient[l] = 0.0;
|
||||
|
||||
int ij = 0;
|
||||
for (int ii = 0; ii < data->natoms; ii++) {
|
||||
for (int ii = 0; ii < data->nlistatoms; ii++) {
|
||||
const int i = data->iatoms[ii];
|
||||
const int ielem = data->ielems[ii];
|
||||
const int elemoffset = data->nparams*ielem;
|
||||
|
||||
415
src/MLIAP/mliap_model_nn.cpp
Normal file
415
src/MLIAP/mliap_model_nn.cpp
Normal file
@ -0,0 +1,415 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Pedro Antonio Santos Flórez (UNLV)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "mliap_model_nn.h"
|
||||
#include "pair_mliap.h"
|
||||
#include "mliap_data.h"
|
||||
#include "error.h"
|
||||
|
||||
#include "comm.h"
|
||||
#include "memory.h"
|
||||
#include "tokenizer.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define MAXLINE 1024
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
MLIAPModelNN::MLIAPModelNN(LAMMPS* lmp, char* coefffilename) :
|
||||
MLIAPModel(lmp, coefffilename)
|
||||
{
|
||||
coeffelem = nullptr;
|
||||
nnodes = nullptr;
|
||||
activation = nullptr;
|
||||
scale = nullptr;
|
||||
if (coefffilename) read_coeffs(coefffilename);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
MLIAPModelNN::~MLIAPModelNN()
|
||||
{
|
||||
memory->destroy(coeffelem);
|
||||
memory->destroy(nnodes);
|
||||
memory->destroy(activation);
|
||||
memory->destroy(scale);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
get number of parameters
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
int MLIAPModelNN::get_nparams()
|
||||
{
|
||||
if (nparams == 0)
|
||||
if (ndescriptors == 0) error->all(FLERR,"ndescriptors not defined");
|
||||
|
||||
return nparams;
|
||||
}
|
||||
|
||||
void MLIAPModelNN::read_coeffs(char *coefffilename)
|
||||
{
|
||||
|
||||
// open coefficient file on proc 0
|
||||
|
||||
FILE *fpcoeff;
|
||||
if (comm->me == 0) {
|
||||
fpcoeff = utils::open_potential(coefffilename,lmp,nullptr);
|
||||
if (fpcoeff == nullptr)
|
||||
error->one(FLERR,fmt::format("Cannot open MLIAPModel coeff file {}: {}",
|
||||
coefffilename,utils::getsyserror()));
|
||||
}
|
||||
|
||||
char line[MAXLINE], *ptr, *tstr;
|
||||
int eof = 0;
|
||||
|
||||
int n;
|
||||
int nwords = 0;
|
||||
while (nwords == 0) {
|
||||
if (comm->me == 0) {
|
||||
ptr = fgets(line,MAXLINE,fpcoeff);
|
||||
if (ptr == nullptr) {
|
||||
eof = 1;
|
||||
fclose(fpcoeff);
|
||||
} else n = strlen(line) + 1;
|
||||
}
|
||||
MPI_Bcast(&eof,1,MPI_INT,0,world);
|
||||
if (eof) break;
|
||||
MPI_Bcast(&n,1,MPI_INT,0,world);
|
||||
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
||||
|
||||
// strip comment, skip line if blank
|
||||
|
||||
if ((ptr = strchr(line,'#'))) *ptr = '\0';
|
||||
nwords = utils::count_words(line);
|
||||
}
|
||||
if (nwords != 2)
|
||||
error->all(FLERR,"Incorrect format in MLIAPModel coefficient file");
|
||||
|
||||
// words = ptrs to all words in line
|
||||
// strip single and double quotes from words
|
||||
|
||||
try {
|
||||
ValueTokenizer coeffs(line);
|
||||
nelements = coeffs.next_int();
|
||||
nparams = coeffs.next_int();
|
||||
} catch (TokenizerException &e) {
|
||||
error->all(FLERR,fmt::format("Incorrect format in MLIAPModel coefficient "
|
||||
"file: {}",e.what()));
|
||||
}
|
||||
|
||||
// set up coeff lists
|
||||
|
||||
memory->create(coeffelem,nelements,nparams,"mliap_snap_model:coeffelem");
|
||||
|
||||
int stats = 0;
|
||||
int ielem = 0;
|
||||
int l = 0;
|
||||
|
||||
while (1) {
|
||||
if (comm->me == 0) {
|
||||
ptr = fgets(line,MAXLINE,fpcoeff);
|
||||
if (ptr == nullptr) {
|
||||
eof = 1;
|
||||
fclose(fpcoeff);
|
||||
} else n = strlen(line) + 1;
|
||||
}
|
||||
|
||||
MPI_Bcast(&eof,1,MPI_INT,0,world);
|
||||
if (eof) break;
|
||||
MPI_Bcast(&n,1,MPI_INT,0,world);
|
||||
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
||||
|
||||
// strip comment, skip line if blank
|
||||
|
||||
if ((ptr = strchr(line,'#'))) *ptr = '\0';
|
||||
nwords = utils::trim_and_count_words(line);
|
||||
if (nwords == 0) continue;
|
||||
|
||||
if (stats == 0) { // Header NET
|
||||
tstr = strtok(line,"' \t\n\r\f");
|
||||
if (strncmp(tstr, "NET", 3) != 0) error->all(FLERR,"Incorrect format in MLIAPModel coefficient file");
|
||||
|
||||
ndescriptors = atoi(strtok(nullptr,"' \t\n\r\f"));
|
||||
nlayers = atoi(strtok(nullptr,"' \t\n\r\f"));
|
||||
|
||||
memory->create(activation,nlayers,"mliap_model:activation");
|
||||
memory->create(nnodes,nlayers,"mliap_model:nnodes");
|
||||
memory->create(scale,nelements,2,ndescriptors,"mliap_model:scale");
|
||||
|
||||
for (int ilayer = 0; ilayer < nlayers; ilayer++) {
|
||||
tstr = strtok(NULL,"' \t\n\r\f");
|
||||
nnodes[ilayer] = atoi(strtok(NULL,"' \t\n\r\f"));
|
||||
|
||||
if (strncmp(tstr, "linear", 6) == 0) activation[ilayer] = 0;
|
||||
else if (strncmp(tstr, "sigmoid", 7) == 0) activation[ilayer] = 1;
|
||||
else if (strncmp(tstr, "tanh", 4) == 0) activation[ilayer] = 2;
|
||||
else if (strncmp(tstr, "relu", 4) == 0) activation[ilayer] = 3;
|
||||
else activation[ilayer] = 4;
|
||||
}
|
||||
|
||||
stats = 1;
|
||||
|
||||
} else if (stats == 1) {
|
||||
scale[ielem][0][l] = atof(strtok(line,"' \t\n\r\f"));
|
||||
for (int icoeff = 1; icoeff < nwords; icoeff++) {
|
||||
scale[ielem][0][l+icoeff] = atof(strtok(nullptr,"' \t\n\r\f"));
|
||||
}
|
||||
l += nwords;
|
||||
if (l == ndescriptors) {
|
||||
stats = 2;
|
||||
l = 0;
|
||||
}
|
||||
|
||||
} else if (stats == 2) {
|
||||
scale[ielem][1][l] = atof(strtok(line,"' \t\n\r\f"));
|
||||
for (int icoeff = 1; icoeff < nwords; icoeff++) {
|
||||
scale[ielem][1][l+icoeff] = atof(strtok(nullptr,"' \t\n\r\f"));
|
||||
}
|
||||
l += nwords;
|
||||
if (l == ndescriptors) {
|
||||
stats = 3;
|
||||
l = 0;
|
||||
}
|
||||
|
||||
// set up coeff lists
|
||||
|
||||
} else if (stats == 3) {
|
||||
if (nwords > 30) error->all(FLERR,"Incorrect format in MLIAPModel coefficient file");
|
||||
|
||||
coeffelem[ielem][l] = atof(strtok(line,"' \t\n\r\f"));
|
||||
for (int icoeff = 1; icoeff < nwords; icoeff++) {
|
||||
coeffelem[ielem][l+icoeff] = atof(strtok(nullptr,"' \t\n\r\f"));
|
||||
}
|
||||
l += nwords;
|
||||
if (l == nparams) {
|
||||
stats = 1;
|
||||
l = 0;
|
||||
ielem++;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Calculate model gradients w.r.t descriptors
|
||||
for each atom beta_i = dE(B_i)/dB_i
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
void MLIAPModelNN::compute_gradients(MLIAPData* data)
|
||||
{
|
||||
data->energy = 0.0;
|
||||
|
||||
for (int ii = 0; ii < data->nlistatoms; ii++) {
|
||||
const int ielem = data->ielems[ii];
|
||||
const int nl = nlayers;
|
||||
|
||||
double* coeffi = coeffelem[ielem];
|
||||
double** scalei = scale[ielem];
|
||||
double **nodes, **dnodes, **bnodes;
|
||||
|
||||
nodes = new double*[nl];
|
||||
dnodes = new double*[nl];
|
||||
bnodes = new double*[nl];
|
||||
for (int l=0; l<nl; ++l) {
|
||||
nodes[l] = new double[nnodes[l]];
|
||||
dnodes[l] = new double[nnodes[l]];
|
||||
bnodes[l] = new double[nnodes[l]];
|
||||
}
|
||||
|
||||
// forwardprop
|
||||
// input - hidden1
|
||||
|
||||
for (int n=0; n < nnodes[0]; n++) {
|
||||
nodes[0][n] = 0;
|
||||
for (int icoeff = 0; icoeff < data->ndescriptors; icoeff++) {
|
||||
nodes[0][n] += coeffi[n*((data->ndescriptors)+1)+icoeff+1] *
|
||||
(data->descriptors[ii][icoeff] - scalei[0][icoeff]) /
|
||||
scalei[1][icoeff];
|
||||
}
|
||||
if (activation[0] == 1) {
|
||||
nodes[0][n] = sigm(nodes[0][n] +
|
||||
coeffi[n*((data->ndescriptors)+1)],
|
||||
dnodes[0][n]);
|
||||
}
|
||||
else if (activation[0] == 2) {
|
||||
nodes[0][n] = tanh(nodes[0][n] +
|
||||
coeffi[n*((data->ndescriptors)+1)],
|
||||
dnodes[0][n]);
|
||||
}
|
||||
else if (activation[0] == 3) {
|
||||
nodes[0][n] = relu(nodes[0][n] +
|
||||
coeffi[n*((data->ndescriptors)+1)],
|
||||
dnodes[0][n]);
|
||||
}
|
||||
else {
|
||||
nodes[0][n] += coeffi[n*((data->ndescriptors)+1)];
|
||||
dnodes[0][n] = 1;
|
||||
}
|
||||
}
|
||||
|
||||
// hidden~output
|
||||
|
||||
int k = 0;
|
||||
if (nl > 1) {
|
||||
k += ((data->ndescriptors)+1)*nnodes[0];
|
||||
for (int l=1; l < nl; l++) {
|
||||
for (int n=0; n < nnodes[l]; n++) {
|
||||
nodes[l][n] = 0;
|
||||
for (int j=0; j < nnodes[l-1]; j++) {
|
||||
nodes[l][n] += coeffi[k+n*(nnodes[l-1]+1)+j+1] *
|
||||
nodes[l-1][j];
|
||||
}
|
||||
if (activation[l] == 1) {
|
||||
nodes[l][n] = sigm(nodes[l][n] +
|
||||
coeffi[k+n*(nnodes[l-1]+1)],
|
||||
dnodes[l][n]);
|
||||
}
|
||||
else if (activation[l] == 2) {
|
||||
nodes[l][n] = tanh(nodes[l][n] +
|
||||
coeffi[k+n*(nnodes[l-1]+1)],
|
||||
dnodes[l][n]);
|
||||
}
|
||||
else if (activation[l] == 3) {
|
||||
nodes[l][n] = relu(nodes[l][n] +
|
||||
coeffi[k+n*(nnodes[l-1]+1)],
|
||||
dnodes[l][n]);
|
||||
}
|
||||
else {
|
||||
nodes[l][n] += coeffi[k+n*(nnodes[l-1]+1)];
|
||||
dnodes[l][n] = 1;
|
||||
}
|
||||
}
|
||||
k += (nnodes[l-1]+1)*nnodes[l];
|
||||
}
|
||||
}
|
||||
|
||||
// backwardprop
|
||||
// output layer dnode initialized to 1.
|
||||
|
||||
for (int n=0; n<nnodes[nl-1]; n++) {
|
||||
if (activation[nl-1] == 0) {
|
||||
bnodes[nl-1][n] = 1;
|
||||
}
|
||||
else {
|
||||
bnodes[nl-1][n] = dnodes[nl-1][n];
|
||||
}
|
||||
}
|
||||
|
||||
if (nl > 1) {
|
||||
for (int l=nl-1; l>0; l--) {
|
||||
k -= (nnodes[l-1]+1)*nnodes[l];
|
||||
for (int n=0; n<nnodes[l-1]; n++) {
|
||||
bnodes[l-1][n] = 0;
|
||||
for (int j=0; j<nnodes[l]; j++) {
|
||||
bnodes[l-1][n] += coeffi[k+j*(nnodes[l-1]+1)+n+1] *
|
||||
bnodes[l][j];
|
||||
}
|
||||
if (activation[l-1] >= 1) {
|
||||
bnodes[l-1][n] *= dnodes[l-1][n];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
for (int icoeff = 0; icoeff < data->ndescriptors; icoeff++) {
|
||||
data->betas[ii][icoeff] = 0;
|
||||
for (int j=0; j<nnodes[0]; j++) {
|
||||
data->betas[ii][icoeff] +=
|
||||
coeffi[j*((data->ndescriptors)+1)+icoeff+1] *
|
||||
bnodes[0][j];
|
||||
}
|
||||
data->betas[ii][icoeff] = data->betas[ii][icoeff]/scalei[1][icoeff];
|
||||
}
|
||||
|
||||
if (data->eflag) {
|
||||
|
||||
// energy of atom I (E_i)
|
||||
|
||||
double etmp = nodes[nl-1][0];
|
||||
|
||||
data->energy += etmp;
|
||||
data->eatoms[ii] = etmp;
|
||||
}
|
||||
// Deleting the variables
|
||||
|
||||
for (int n=0; n<nl; n++) {
|
||||
delete nodes[n];
|
||||
delete dnodes[n];
|
||||
delete bnodes[n];
|
||||
}
|
||||
|
||||
delete nodes;
|
||||
delete dnodes;
|
||||
delete bnodes;
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Calculate model double gradients w.r.t descriptors and parameters
|
||||
for each atom energy gamma_lk = d2E(B)/dB_k/dsigma_l,
|
||||
where sigma_l is a parameter, B_k a descriptor,
|
||||
and atom subscript i is omitted
|
||||
|
||||
gamma is in CSR format:
|
||||
nnz = number of non-zero values
|
||||
gamma_row_index[inz] = l indices, 0 <= l < nparams
|
||||
gamma_col_indexiinz] = k indices, 0 <= k < ndescriptors
|
||||
gamma[i][inz] = non-zero values, 0 <= inz < nnz
|
||||
|
||||
egradient is derivative of energy w.r.t. parameters
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
void MLIAPModelNN::compute_gradgrads(class MLIAPData* data)
|
||||
{
|
||||
error->all(FLERR,"compute_gradgrads not implemented");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
calculate gradients of forces w.r.t. parameters
|
||||
egradient is derivative of energy w.r.t. parameters
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
void MLIAPModelNN::compute_force_gradients(class MLIAPData* data)
|
||||
{
|
||||
error->all(FLERR,"compute_force_gradients not implemented");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
count the number of non-zero entries in gamma matrix
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
int MLIAPModelNN::get_gamma_nnz(class MLIAPData* data)
|
||||
{
|
||||
// todo: get_gamma_nnz
|
||||
return 0;
|
||||
}
|
||||
|
||||
double MLIAPModelNN::memory_usage()
|
||||
{
|
||||
double bytes = 0;
|
||||
|
||||
bytes += (double)nelements*nparams*sizeof(double); // coeffelem
|
||||
bytes += (double)nelements*2*ndescriptors*sizeof(double); // scale
|
||||
bytes += (int)nlayers*sizeof(int); // nnodes
|
||||
bytes += (int)nlayers*sizeof(int); // activation
|
||||
return bytes;
|
||||
}
|
||||
68
src/MLIAP/mliap_model_nn.h
Normal file
68
src/MLIAP/mliap_model_nn.h
Normal file
@ -0,0 +1,68 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_MLIAP_MODEL_NN_H
|
||||
#define LMP_MLIAP_MODEL_NN_H
|
||||
|
||||
#include "mliap_model.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class MLIAPModelNN : public MLIAPModel {
|
||||
public:
|
||||
MLIAPModelNN(LAMMPS*, char* = nullptr);
|
||||
~MLIAPModelNN();
|
||||
virtual int get_nparams();
|
||||
virtual int get_gamma_nnz(class MLIAPData*);
|
||||
virtual void compute_gradients(class MLIAPData*);
|
||||
virtual void compute_gradgrads(class MLIAPData*);
|
||||
virtual void compute_force_gradients(class MLIAPData*);
|
||||
virtual double memory_usage();
|
||||
|
||||
int nlayers; // number of layers per element
|
||||
|
||||
protected:
|
||||
int *activation; // activation functions
|
||||
int *nnodes; // number of nodes per layer
|
||||
double ***scale; // element scale values
|
||||
double **coeffelem; // element coefficients
|
||||
virtual void read_coeffs(char *);
|
||||
|
||||
inline double sigm(double x, double &deriv) {
|
||||
double expl = 1./(1.+exp(-x));
|
||||
deriv = expl*(1-expl);
|
||||
return expl;
|
||||
}
|
||||
|
||||
inline double tanh(double x, double &deriv) {
|
||||
double expl = 2./(1.+exp(-2.*x))-1;
|
||||
deriv = 1.-expl*expl;
|
||||
return expl;
|
||||
}
|
||||
|
||||
inline double relu(double x, double &deriv) {
|
||||
if (x > 0) {
|
||||
deriv = 1.;
|
||||
return x;
|
||||
} else {
|
||||
deriv = 0.;
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
@ -17,7 +17,7 @@ from libcpp.string cimport string
|
||||
cdef extern from "mliap_data.h" namespace "LAMMPS_NS":
|
||||
cdef cppclass MLIAPData:
|
||||
# Array shapes
|
||||
int natoms
|
||||
int nlistatoms
|
||||
int ndescriptors
|
||||
|
||||
# Input data
|
||||
@ -103,7 +103,7 @@ cdef public void MLIAPPY_compute_gradients(MLIAPModelPython * c_model, MLIAPData
|
||||
model = retrieve(c_model)
|
||||
|
||||
n_d = data.ndescriptors
|
||||
n_a = data.natoms
|
||||
n_a = data.nlistatoms
|
||||
|
||||
# Make numpy arrays from pointers
|
||||
beta_np = np.asarray(<double[:n_a,:n_d] > &data.betas[0][0])
|
||||
|
||||
@ -59,7 +59,7 @@ void MLIAPModelQuadratic::compute_gradients(MLIAPData* data)
|
||||
{
|
||||
data->energy = 0.0;
|
||||
|
||||
for (int ii = 0; ii < data->natoms; ii++) {
|
||||
for (int ii = 0; ii < data->nlistatoms; ii++) {
|
||||
const int ielem = data->ielems[ii];
|
||||
|
||||
double* coeffi = coeffelem[ielem];
|
||||
@ -133,7 +133,7 @@ void MLIAPModelQuadratic::compute_gradgrads(class MLIAPData* data)
|
||||
for (int l = 0; l < data->nelements*data->nparams; l++)
|
||||
data->egradient[l] = 0.0;
|
||||
|
||||
for (int ii = 0; ii < data->natoms; ii++) {
|
||||
for (int ii = 0; ii < data->nlistatoms; ii++) {
|
||||
const int ielem = data->ielems[ii];
|
||||
const int elemoffset = data->nparams*ielem;
|
||||
|
||||
@ -215,7 +215,7 @@ void MLIAPModelQuadratic::compute_force_gradients(class MLIAPData* data) {
|
||||
data->egradient[l] = 0.0;
|
||||
|
||||
int ij = 0;
|
||||
for (int ii = 0; ii < data->natoms; ii++) {
|
||||
for (int ii = 0; ii < data->nlistatoms; ii++) {
|
||||
const int i = data->iatoms[ii];
|
||||
const int ielem = data->ielems[ii];
|
||||
const int elemoffset = data->nparams*ielem;
|
||||
|
||||
@ -20,6 +20,7 @@
|
||||
#include "mliap_data.h"
|
||||
#include "mliap_model_linear.h"
|
||||
#include "mliap_model_quadratic.h"
|
||||
#include "mliap_model_nn.h"
|
||||
#include "mliap_descriptor_snap.h"
|
||||
#ifdef MLIAP_PYTHON
|
||||
#include "mliap_model_python.h"
|
||||
@ -152,6 +153,10 @@ void PairMLIAP::settings(int narg, char ** arg)
|
||||
if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command");
|
||||
model = new MLIAPModelQuadratic(lmp,arg[iarg+2]);
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg+1],"nn") == 0) {
|
||||
if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command");
|
||||
model = new MLIAPModelNN(lmp,arg[iarg+2]);
|
||||
iarg += 3;
|
||||
#ifdef MLIAP_PYTHON
|
||||
} else if (strcmp(arg[iarg+1],"mliappy") == 0) {
|
||||
if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command");
|
||||
@ -250,7 +255,7 @@ void PairMLIAP::e_tally(MLIAPData* data)
|
||||
{
|
||||
if (eflag_global) eng_vdwl += data->energy;
|
||||
if (eflag_atom)
|
||||
for (int ii = 0; ii < data->natoms; ii++) {
|
||||
for (int ii = 0; ii < data->nlistatoms; ii++) {
|
||||
const int i = data->iatoms[ii];
|
||||
eatom[i] += data->eatoms[ii];
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user