Loading doc/src/compute_mliap.rst +23 −16 Original line number Diff line number Diff line Loading @@ -12,25 +12,25 @@ Syntax * ID, group-ID are documented in :doc:`compute <compute>` command * mliap = style name of this compute command * two keyword/value pairs must be appended * keyword = *model* or *descriptor* * two or more keyword/value pairs must be appended * keyword = *model* or *descriptor* or *gradgradflag* .. parsed-literal:: *model* values = style Nelems Nparams *model* values = style style = *linear* or *quadratic* Nelems = number of elements Nparams = number of parameters per element *descriptor* values = style filename style = *sna* filename = name of file containing descriptor definitions *gradgradflag* value = 0/1 toggle gradgrad method for force gradient Examples """""""" .. code-block:: LAMMPS compute mliap model linear 2 31 descriptor sna Ta06A.mliap.descriptor compute mliap model linear descriptor sna Ta06A.mliap.descriptor Description """"""""""" Loading @@ -57,20 +57,13 @@ The compute *mliap* command must be followed by two keywords *model* and *descriptor* in either order. The *model* keyword is followed by a model style, currently limited to either *linear* or *quadratic*. In both cases, this is followed by two arguments. *nelems* is the number of elements. It must be equal to the number of LAMMPS atom types. *nparams* is the number of parameters per element for this model i.e. the number of parameter gradients for each element. Note these definitions are identical to those of *nelems* and *nparams* in the :doc:`pair_style mliap <pair_mliap>` model file. either *linear* or *quadratic*. The *descriptor* keyword is followed by a descriptor style, and additional arguments. Currently the only descriptor style is *sna*, indicating the bispectrum component descriptors used by the Spectral Neighbor Analysis Potential (SNAP) potentials of :doc:`pair_style snap <pair_snap>`. The \'p\' in SNAP is dropped, because keywords that match pair_styles are silently stripped out by the LAMMPS command parser. A single additional argument specifies the descriptor filename A single additional argument specifies the descriptor filename containing the parameters and setting used by the SNAP descriptor. The descriptor filename usually ends in the *.mliap.descriptor* extension. The format of this file is identical to the descriptor file in the Loading Loading @@ -109,6 +102,17 @@ command: See section below on output for a detailed explanation of the data layout in the global array. The optional keyword *gradgradflag* controls how the force gradient is calculated. A value of 1 requires that the model provide the matrix of double gradients of energy w.r.t. both parameters and descriptors. For the linear and quadratic models this matrix is sparse and so is easily calculated and stored. For other models, this matrix may be prohibitively expensive to calculate and store. A value of 0 requires that the descriptor provide the derivative of the descriptors w.r.t. the position of every neighbor atom. This is not optimal for linear and quadratic models, but may be a better choice for more complex models. Atoms not in the group do not contribute to this compute. Neighbor atoms not in the group do not contribute to this compute. The neighbor list needed to compute this quantity is constructed each Loading Loading @@ -167,4 +171,7 @@ Related commands :doc:`pair_style mliap <pair_mliap>` **Default:** none Default """"""" The keyword defaults are gradgradflag = 1 doc/src/pair_mliap.rst +1 −2 Original line number Diff line number Diff line Loading @@ -86,8 +86,7 @@ The *descriptor* keyword is followed by a descriptor style, and additional argum Currently the only descriptor style is *sna*, indicating the bispectrum component descriptors used by the Spectral Neighbor Analysis Potential (SNAP) potentials of :doc:`pair_style snap <pair_snap>`. The \'p\' in SNAP is dropped, because keywords that match pair_styles are silently stripped out by the LAMMPS command parser. A single additional argument specifies the descriptor filename A single additional argument specifies the descriptor filename containing the parameters and setting used by the SNAP descriptor. The descriptor filename usually ends in the *.mliap.descriptor* extension. Loading doc/utils/sphinx-config/false_positives.txt +1 −0 Original line number Diff line number Diff line Loading @@ -1075,6 +1075,7 @@ GPa gpu gpuID gpus gradgradflag gradV GradVidottan graining Loading examples/mliap/in.mliap.quadratic.compute +20 −10 Original line number Diff line number Diff line Loading @@ -67,13 +67,6 @@ compute vbsum all reduce sum c_vb[*] # fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector variable db_2_100 equal c_db[2][100] # set up compute snap generating global array compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.dat mode vector thermo 100 # test output: 1: total potential energy # 2: xy component of stress tensor # 3: Sum(0.5*(B_{222}^i)^2, all i of type 2) Loading @@ -81,15 +74,32 @@ thermo 100 # 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2) # # followed by 5 counterparts from compute snap thermo 100 # run compute mliap with gradgradflag = 1 compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 1 fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg1.dat mode vector thermo_style custom & pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 & c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42] thermo_modify norm no # dump mydump_db all custom 1000 dump_db id c_db[*] # dump_modify mydump_db sort id run ${nsteps} uncompute snap unfix snap # run compute mliap with gradgradflag = 0 # Run MD compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 0 fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg0.dat mode vector thermo_style custom & pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 & c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42] thermo_modify norm no run ${nsteps} examples/mliap/in.mliap.snap.compute +18 −8 Original line number Diff line number Diff line Loading @@ -67,11 +67,6 @@ compute vbsum all reduce sum c_vb[*] # fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector variable db_2_25 equal c_db[2][25] # set up compute snap generating global array compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector thermo 100 # test output: 1: total potential energy Loading @@ -82,14 +77,29 @@ thermo 100 # # followed by 5 counterparts from compute snap # run compute mliap with gradgradflag = 1 compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 1 fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg1.dat mode vector thermo_style custom & pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 & c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12] thermo_modify norm no # dump mydump_db all custom 1000 dump_db id c_db[*] # dump_modify mydump_db sort id run ${nsteps} uncompute snap unfix snap # Run MD # run compute mliap with gradgradflag = 0 compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 0 fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg0.dat mode vector thermo_style custom & pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 & c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12] thermo_modify norm no run ${nsteps} Loading
doc/src/compute_mliap.rst +23 −16 Original line number Diff line number Diff line Loading @@ -12,25 +12,25 @@ Syntax * ID, group-ID are documented in :doc:`compute <compute>` command * mliap = style name of this compute command * two keyword/value pairs must be appended * keyword = *model* or *descriptor* * two or more keyword/value pairs must be appended * keyword = *model* or *descriptor* or *gradgradflag* .. parsed-literal:: *model* values = style Nelems Nparams *model* values = style style = *linear* or *quadratic* Nelems = number of elements Nparams = number of parameters per element *descriptor* values = style filename style = *sna* filename = name of file containing descriptor definitions *gradgradflag* value = 0/1 toggle gradgrad method for force gradient Examples """""""" .. code-block:: LAMMPS compute mliap model linear 2 31 descriptor sna Ta06A.mliap.descriptor compute mliap model linear descriptor sna Ta06A.mliap.descriptor Description """"""""""" Loading @@ -57,20 +57,13 @@ The compute *mliap* command must be followed by two keywords *model* and *descriptor* in either order. The *model* keyword is followed by a model style, currently limited to either *linear* or *quadratic*. In both cases, this is followed by two arguments. *nelems* is the number of elements. It must be equal to the number of LAMMPS atom types. *nparams* is the number of parameters per element for this model i.e. the number of parameter gradients for each element. Note these definitions are identical to those of *nelems* and *nparams* in the :doc:`pair_style mliap <pair_mliap>` model file. either *linear* or *quadratic*. The *descriptor* keyword is followed by a descriptor style, and additional arguments. Currently the only descriptor style is *sna*, indicating the bispectrum component descriptors used by the Spectral Neighbor Analysis Potential (SNAP) potentials of :doc:`pair_style snap <pair_snap>`. The \'p\' in SNAP is dropped, because keywords that match pair_styles are silently stripped out by the LAMMPS command parser. A single additional argument specifies the descriptor filename A single additional argument specifies the descriptor filename containing the parameters and setting used by the SNAP descriptor. The descriptor filename usually ends in the *.mliap.descriptor* extension. The format of this file is identical to the descriptor file in the Loading Loading @@ -109,6 +102,17 @@ command: See section below on output for a detailed explanation of the data layout in the global array. The optional keyword *gradgradflag* controls how the force gradient is calculated. A value of 1 requires that the model provide the matrix of double gradients of energy w.r.t. both parameters and descriptors. For the linear and quadratic models this matrix is sparse and so is easily calculated and stored. For other models, this matrix may be prohibitively expensive to calculate and store. A value of 0 requires that the descriptor provide the derivative of the descriptors w.r.t. the position of every neighbor atom. This is not optimal for linear and quadratic models, but may be a better choice for more complex models. Atoms not in the group do not contribute to this compute. Neighbor atoms not in the group do not contribute to this compute. The neighbor list needed to compute this quantity is constructed each Loading Loading @@ -167,4 +171,7 @@ Related commands :doc:`pair_style mliap <pair_mliap>` **Default:** none Default """"""" The keyword defaults are gradgradflag = 1
doc/src/pair_mliap.rst +1 −2 Original line number Diff line number Diff line Loading @@ -86,8 +86,7 @@ The *descriptor* keyword is followed by a descriptor style, and additional argum Currently the only descriptor style is *sna*, indicating the bispectrum component descriptors used by the Spectral Neighbor Analysis Potential (SNAP) potentials of :doc:`pair_style snap <pair_snap>`. The \'p\' in SNAP is dropped, because keywords that match pair_styles are silently stripped out by the LAMMPS command parser. A single additional argument specifies the descriptor filename A single additional argument specifies the descriptor filename containing the parameters and setting used by the SNAP descriptor. The descriptor filename usually ends in the *.mliap.descriptor* extension. Loading
doc/utils/sphinx-config/false_positives.txt +1 −0 Original line number Diff line number Diff line Loading @@ -1075,6 +1075,7 @@ GPa gpu gpuID gpus gradgradflag gradV GradVidottan graining Loading
examples/mliap/in.mliap.quadratic.compute +20 −10 Original line number Diff line number Diff line Loading @@ -67,13 +67,6 @@ compute vbsum all reduce sum c_vb[*] # fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector variable db_2_100 equal c_db[2][100] # set up compute snap generating global array compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.dat mode vector thermo 100 # test output: 1: total potential energy # 2: xy component of stress tensor # 3: Sum(0.5*(B_{222}^i)^2, all i of type 2) Loading @@ -81,15 +74,32 @@ thermo 100 # 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2) # # followed by 5 counterparts from compute snap thermo 100 # run compute mliap with gradgradflag = 1 compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 1 fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg1.dat mode vector thermo_style custom & pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 & c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42] thermo_modify norm no # dump mydump_db all custom 1000 dump_db id c_db[*] # dump_modify mydump_db sort id run ${nsteps} uncompute snap unfix snap # run compute mliap with gradgradflag = 0 # Run MD compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 0 fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg0.dat mode vector thermo_style custom & pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 & c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42] thermo_modify norm no run ${nsteps}
examples/mliap/in.mliap.snap.compute +18 −8 Original line number Diff line number Diff line Loading @@ -67,11 +67,6 @@ compute vbsum all reduce sum c_vb[*] # fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector variable db_2_25 equal c_db[2][25] # set up compute snap generating global array compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector thermo 100 # test output: 1: total potential energy Loading @@ -82,14 +77,29 @@ thermo 100 # # followed by 5 counterparts from compute snap # run compute mliap with gradgradflag = 1 compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 1 fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg1.dat mode vector thermo_style custom & pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 & c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12] thermo_modify norm no # dump mydump_db all custom 1000 dump_db id c_db[*] # dump_modify mydump_db sort id run ${nsteps} uncompute snap unfix snap # Run MD # run compute mliap with gradgradflag = 0 compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 0 fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg0.dat mode vector thermo_style custom & pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 & c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12] thermo_modify norm no run ${nsteps}
