Finished cleaning up and testing. MLIAPData class is now fully integrated with... (095c6a98) · Commits · 郑智淋 / lammps

doc/src/compute_mliap.rst

+4 −12

Original line number	Original line	Diff line number	Diff line
	@@ -17,10 +17,8 @@ Syntax

	.. parsed-literal::		.. parsed-literal::

	model values = style Nelems Nparams		model values = style
	style = linear or quadratic		style = linear or quadratic
	Nelems = number of elements
	Nparams = number of parameters per element
	descriptor values = style filename		descriptor values = style filename
	style = sna		style = sna
	filename = name of file containing descriptor definitions		filename = name of file containing descriptor definitions
	@@ -31,7 +29,7 @@ Examples

	.. code-block:: LAMMPS		.. code-block:: LAMMPS

	compute mliap model linear 2 31 descriptor sna Ta06A.mliap.descriptor		compute mliap model linear descriptor sna Ta06A.mliap.descriptor

	Description		Description
	"""""""""""		"""""""""""
	@@ -58,13 +56,7 @@ The compute mliap command must be followed by two keywords
	model and descriptor in either order.		model and descriptor in either order.

	The model keyword is followed by a model style, currently limited to		The model keyword is followed by a model style, currently limited to
	either linear or quadratic. In both cases,		either linear or quadratic.
	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.

	The descriptor keyword is followed by a descriptor style, and additional arguments.		The descriptor keyword is followed by a descriptor style, and additional arguments.
	Currently the only descriptor style is sna, indicating the bispectrum component		Currently the only descriptor style is sna, indicating the bispectrum component

examples/mliap/in.mliap.quadratic.compute

+2 −2

Original line number	Original line	Diff line number	Diff line
	@@ -78,7 +78,7 @@ thermo 100

	# run compute mliap with gradgradflag = 1		# run compute mliap with gradgradflag = 1

	compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 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		fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg1.dat mode vector

	thermo_style custom &		thermo_style custom &
	@@ -93,7 +93,7 @@ unfix snap

	# run compute mliap with gradgradflag = 0		# run compute mliap with gradgradflag = 0

	compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0		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		fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg0.dat mode vector

	thermo_style custom &		thermo_style custom &

examples/mliap/in.mliap.snap.compute

+2 −2

Original line number	Original line	Diff line number	Diff line
	@@ -79,7 +79,7 @@ thermo 100

	# run compute mliap with gradgradflag = 1		# run compute mliap with gradgradflag = 1

	compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 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		fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg1.dat mode vector

	thermo_style custom &		thermo_style custom &
	@@ -94,7 +94,7 @@ unfix snap

	# run compute mliap with gradgradflag = 0		# run compute mliap with gradgradflag = 0

	compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 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		fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg0.dat mode vector

	thermo_style custom &		thermo_style custom &

examples/mliap/log.03Jul20.mliap.quadratic.compute.g++.1

+7 −7

Original line number	Original line	Diff line number	Diff line
	@@ -110,7 +110,7 @@ thermo 100

	# run compute mliap with gradgradflag = 1		# run compute mliap with gradgradflag = 1

	compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 1		compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 1
	SNAP keyword rcutfac 1.0		SNAP keyword rcutfac 1.0
	SNAP keyword twojmax 2		SNAP keyword twojmax 2
	SNAP keyword nelems 2		SNAP keyword nelems 2
	@@ -160,7 +160,7 @@ Neighbor list info ...
	pair build: full/bin/atomonly		pair build: full/bin/atomonly
	stencil: full/bin/3d		stencil: full/bin/3d
	bin: standard		bin: standard
	Per MPI rank memory allocation (min/avg/max) = 22.45 \| 22.45 \| 22.45 Mbytes		Per MPI rank memory allocation (min/avg/max) = 22.47 \| 22.47 \| 22.47 Mbytes
	PotEng 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]		PotEng 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]
	322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035		322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
	Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms		Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms
	@@ -196,7 +196,7 @@ unfix snap

	# run compute mliap with gradgradflag = 0		# run compute mliap with gradgradflag = 0

	compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0		compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 0
	SNAP keyword rcutfac 1.0		SNAP keyword rcutfac 1.0
	SNAP keyword twojmax 2		SNAP keyword twojmax 2
	SNAP keyword nelems 2		SNAP keyword nelems 2
	@@ -247,12 +247,12 @@ Neighbor list info ...
	pair build: full/bin/atomonly		pair build: full/bin/atomonly
	stencil: full/bin/3d		stencil: full/bin/3d
	bin: standard		bin: standard
	Per MPI rank memory allocation (min/avg/max) = 70.2 \| 70.2 \| 70.2 Mbytes		Per MPI rank memory allocation (min/avg/max) = 70.24 \| 70.24 \| 70.24 Mbytes
	PotEng 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]		PotEng 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]
	322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035		322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
	Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms		Loop time of 2e-06 on 1 procs for 0 steps with 2 atoms

	200.0% CPU use with 1 MPI tasks x no OpenMP threads		50.0% CPU use with 1 MPI tasks x no OpenMP threads

	MPI task timing breakdown:		MPI task timing breakdown:
	Section \| min time \| avg time \| max time \|%varavg\| %total		Section \| min time \| avg time \| max time \|%varavg\| %total
	@@ -262,7 +262,7 @@ Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
	Comm \| 0 \| 0 \| 0 \| 0.0 \| 0.00		Comm \| 0 \| 0 \| 0 \| 0.0 \| 0.00
	Output \| 0 \| 0 \| 0 \| 0.0 \| 0.00		Output \| 0 \| 0 \| 0 \| 0.0 \| 0.00
	Modify \| 0 \| 0 \| 0 \| 0.0 \| 0.00		Modify \| 0 \| 0 \| 0 \| 0.0 \| 0.00
	Other \| \| 1e-06 \| \| \|100.00		Other \| \| 2e-06 \| \| \|100.00

	Nlocal: 2.0 ave 2.0 max 2.0 min		Nlocal: 2.0 ave 2.0 max 2.0 min
	Histogram: 1 0 0 0 0 0 0 0 0 0		Histogram: 1 0 0 0 0 0 0 0 0 0

examples/mliap/log.03Jul20.mliap.quadratic.compute.g++.4

+10 −10

Original line number	Original line	Diff line number	Diff line
	@@ -110,7 +110,7 @@ thermo 100

	# run compute mliap with gradgradflag = 1		# run compute mliap with gradgradflag = 1

	compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 1		compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 1
	SNAP keyword rcutfac 1.0		SNAP keyword rcutfac 1.0
	SNAP keyword twojmax 2		SNAP keyword twojmax 2
	SNAP keyword nelems 2		SNAP keyword nelems 2
	@@ -161,12 +161,12 @@ Neighbor list info ...
	stencil: full/bin/3d		stencil: full/bin/3d
	bin: standard		bin: standard
	WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)		WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
	Per MPI rank memory allocation (min/avg/max) = 22.18 \| 22.18 \| 22.18 Mbytes		Per MPI rank memory allocation (min/avg/max) = 6.429 \| 6.43 \| 6.432 Mbytes
	PotEng 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]		PotEng 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]
	322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035		322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
	Loop time of 3.5e-06 on 4 procs for 0 steps with 2 atoms		Loop time of 4.25e-06 on 4 procs for 0 steps with 2 atoms

	92.9% CPU use with 4 MPI tasks x no OpenMP threads		82.4% CPU use with 4 MPI tasks x no OpenMP threads

	MPI task timing breakdown:		MPI task timing breakdown:
	Section \| min time \| avg time \| max time \|%varavg\| %total		Section \| min time \| avg time \| max time \|%varavg\| %total
	@@ -176,7 +176,7 @@ Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
	Comm \| 0 \| 0 \| 0 \| 0.0 \| 0.00		Comm \| 0 \| 0 \| 0 \| 0.0 \| 0.00
	Output \| 0 \| 0 \| 0 \| 0.0 \| 0.00		Output \| 0 \| 0 \| 0 \| 0.0 \| 0.00
	Modify \| 0 \| 0 \| 0 \| 0.0 \| 0.00		Modify \| 0 \| 0 \| 0 \| 0.0 \| 0.00
	Other \| \| 3.5e-06 \| \| \|100.00		Other \| \| 4.25e-06 \| \| \|100.00

	Nlocal: 0.5 ave 1.0 max 0.0 min		Nlocal: 0.5 ave 1.0 max 0.0 min
	Histogram: 2 0 0 0 0 0 0 0 0 2		Histogram: 2 0 0 0 0 0 0 0 0 2
	@@ -197,7 +197,7 @@ unfix snap

	# run compute mliap with gradgradflag = 0		# run compute mliap with gradgradflag = 0

	compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0		compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 0
	SNAP keyword rcutfac 1.0		SNAP keyword rcutfac 1.0
	SNAP keyword twojmax 2		SNAP keyword twojmax 2
	SNAP keyword nelems 2		SNAP keyword nelems 2
	@@ -249,12 +249,12 @@ Neighbor list info ...
	stencil: full/bin/3d		stencil: full/bin/3d
	bin: standard		bin: standard
	WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)		WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
	Per MPI rank memory allocation (min/avg/max) = 69.68 \| 69.81 \| 69.93 Mbytes		Per MPI rank memory allocation (min/avg/max) = 53.93 \| 54.06 \| 54.18 Mbytes
	PotEng 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]		PotEng 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]
	322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035		322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
	Loop time of 2.75e-06 on 4 procs for 0 steps with 2 atoms		Loop time of 4e-06 on 4 procs for 0 steps with 2 atoms

	100.0% CPU use with 4 MPI tasks x no OpenMP threads		106.2% CPU use with 4 MPI tasks x no OpenMP threads

	MPI task timing breakdown:		MPI task timing breakdown:
	Section \| min time \| avg time \| max time \|%varavg\| %total		Section \| min time \| avg time \| max time \|%varavg\| %total
	@@ -264,7 +264,7 @@ Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
	Comm \| 0 \| 0 \| 0 \| 0.0 \| 0.00		Comm \| 0 \| 0 \| 0 \| 0.0 \| 0.00
	Output \| 0 \| 0 \| 0 \| 0.0 \| 0.00		Output \| 0 \| 0 \| 0 \| 0.0 \| 0.00
	Modify \| 0 \| 0 \| 0 \| 0.0 \| 0.00		Modify \| 0 \| 0 \| 0 \| 0.0 \| 0.00
	Other \| \| 2.75e-06 \| \| \|100.00		Other \| \| 4e-06 \| \| \|100.00

	Nlocal: 0.5 ave 1.0 max 0.0 min		Nlocal: 0.5 ave 1.0 max 0.0 min
	Histogram: 2 0 0 0 0 0 0 0 0 2		Histogram: 2 0 0 0 0 0 0 0 0 2

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