diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt
index 1c3787e696638191373d0b563f461c37d42dddad..268e23ac2808d82f8750b95bd652cd4d50f6b9d2 100644
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/src/compute_sna_atom.txt
@@ -161,9 +161,9 @@ function.
The keyword {bzeroflag} determines whether or not {B0}, the bispectrum
components of an atom with no neighbors, are subtracted from
-the calculated bispectrum components. This optional keyword is only
-available for compute {sna/atom}, as {snad/atom} and {snav/atom}
-are unaffected by the removal of constant terms.
+the calculated bispectrum components. This optional keyword
+normally only affects compute {sna/atom}. However, when
+{quadraticflag} is on, it also affects {snad/atom} and {snav/atom}.
The keyword {quadraticflag} determines whether or not the
quadratic analogs to the bispectrum quantities are generated.
@@ -230,13 +230,18 @@ are 30, 90, and 180, respectively. With {quadratic} value=1,
the numbers of columns are 930, 2790, and 5580, respectively.
If the {quadratic} keyword value is set to 1, then additional
-columns are appended to each per-atom array, corresponding to
+columns are generated, corresponding to
the products of all distinct pairs of bispectrum components. If the
number of bispectrum components is {K}, then the number of distinct pairs
-is {K}({K}+1)/2. These are output in subblocks of {K}({K}+1)/2 columns, using the same
-ordering of sub-blocks as was used for the bispectrum
-components. Within each sub-block, the ordering is upper-triangular,
-(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K})
+is {K}({K}+1)/2.
+For compute {sna/atom} these columns are appended to existing {K} columns.
+The ordering of quadratic terms is upper-triangular,
+(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}).
+For computes {snad/atom} and {snav/atom} each set of {K}({K}+1)/2
+additional columns is inserted directly after each of sub-block
+of linear terms i.e. linear and quadratic terms are contiguous.
+So the nesting order from inside to outside is bispectrum component,
+linear then quadratic, vector/tensor component, type.
These values can be accessed by any command that uses per-atom values
from a compute as input. See "Section
diff --git a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1 b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..c5e0f6abab7b7eb657e529096265fa9d3a9bfcff
--- /dev/null
+++ b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1
@@ -0,0 +1,127 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.160
+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 3.16
+Lattice spacing in x,y,z = 3.16 3.16 3.16
+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 (12.64 12.64 12.64)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 128 atoms
+ Time spent = 0.000223637 secs
+
+mass 1 183.84
+
+# choose potential
+
+include Mo_Chen_PRM2017.snap
+
+# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# Generated by Materials Virtual Lab
+# Definition of SNAP potential.
+pair_style snap
+pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
+Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
+SNAP Element = Mo, Radius 0.5, Weight 1
+Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
+SNAP keyword rcutfac 4.615858
+SNAP keyword twojmax 6
+
+
+# Setup output
+
+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 = 5.61586
+ ghost atom cutoff = 5.61586
+ binsize = 2.80793, bins = 5 5 5
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) 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) = 3.507 | 3.507 | 3.507 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 300 -22.405975 0 -22.3675 2575.7657
+ 10 294.77555 -22.405305 0 -22.3675 2756.6894
+ 20 279.53011 -22.40335 0 -22.3675 3285.8272
+ 30 255.52174 -22.40027 0 -22.3675 4122.8933
+ 40 224.7299 -22.396321 0 -22.367499 5204.3499
+ 50 189.67529 -22.391825 0 -22.367499 6449.1308
+ 60 153.18862 -22.387145 0 -22.367499 7765.911
+ 70 118.14998 -22.382652 0 -22.367499 9061.1616
+ 80 87.224916 -22.378685 0 -22.367499 10247.68
+ 90 62.623892 -22.37553 0 -22.367498 11250.067
+ 100 45.9103 -22.373386 0 -22.367498 12011.726
+Loop time of 3.3917 on 1 procs for 100 steps with 128 atoms
+
+Performance: 1.274 ns/day, 18.843 hours/ns, 29.484 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.3906 | 3.3906 | 3.3906 | 0.0 | 99.97
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00039721 | 0.00039721 | 0.00039721 | 0.0 | 0.01
+Output | 0.00023007 | 0.00023007 | 0.00023007 | 0.0 | 0.01
+Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.01
+Other | | 0.0002868 | | | 0.01
+
+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: 0 ave 0 max 0 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: 0:00:03
diff --git a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c25f1f5530856ab7dc5492526aa168c9dafd6fad
--- /dev/null
+++ b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4
@@ -0,0 +1,127 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.160
+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 3.16
+Lattice spacing in x,y,z = 3.16 3.16 3.16
+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 (12.64 12.64 12.64)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 128 atoms
+ Time spent = 0.000277281 secs
+
+mass 1 183.84
+
+# choose potential
+
+include Mo_Chen_PRM2017.snap
+
+# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# Generated by Materials Virtual Lab
+# Definition of SNAP potential.
+pair_style snap
+pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
+Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
+SNAP Element = Mo, Radius 0.5, Weight 1
+Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
+SNAP keyword rcutfac 4.615858
+SNAP keyword twojmax 6
+
+
+# Setup output
+
+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 = 5.61586
+ ghost atom cutoff = 5.61586
+ binsize = 2.80793, bins = 5 5 5
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) 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) = 3.486 | 3.486 | 3.486 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 300 -22.405975 0 -22.3675 2575.7657
+ 10 294.63153 -22.405286 0 -22.3675 2753.4662
+ 20 278.98535 -22.40328 0 -22.3675 3272.416
+ 30 254.38916 -22.400125 0 -22.3675 4091.8933
+ 40 222.91191 -22.396088 0 -22.367499 5148.5505
+ 50 187.16984 -22.391504 0 -22.367499 6362.2454
+ 60 150.08253 -22.386747 0 -22.367499 7643.2732
+ 70 114.60307 -22.382197 0 -22.367499 8900.2448
+ 80 83.449257 -22.378201 0 -22.367499 10047.619
+ 90 58.862643 -22.375048 0 -22.367498 11012.233
+ 100 42.41931 -22.372939 0 -22.367498 11740.641
+Loop time of 1.91636 on 4 procs for 100 steps with 128 atoms
+
+Performance: 2.254 ns/day, 10.646 hours/ns, 52.182 timesteps/s
+97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.8147 | 1.8411 | 1.8875 | 2.1 | 96.07
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.022276 | 0.069629 | 0.095057 | 10.7 | 3.63
+Output | 0.00032496 | 0.00065821 | 0.0016179 | 0.0 | 0.03
+Modify | 0.00019503 | 0.00020915 | 0.00023341 | 0.0 | 0.01
+Other | | 0.00481 | | | 0.25
+
+Nlocal: 32 ave 32 max 32 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 431 ave 431 max 431 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 1856 ave 1856 max 1856 min
+Histogram: 4 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
diff --git a/examples/snap/log.5Oct16.snap.Ta06A.g++.1 b/examples/snap/log.20Apr18.snap.Ta06A.g++.1
similarity index 71%
rename from examples/snap/log.5Oct16.snap.Ta06A.g++.1
rename to examples/snap/log.20Apr18.snap.Ta06A.g++.1
index 647ffac8b4326efa8ce7f6fca6b4ee9e577d32f5..d2296852a051bc6d12c58924a802357574a47d6e 100644
--- a/examples/snap/log.5Oct16.snap.Ta06A.g++.1
+++ b/examples/snap/log.20Apr18.snap.Ta06A.g++.1
@@ -1,4 +1,6 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@@ -31,12 +33,13 @@ 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
+ Time spent = 0.000328064 secs
mass 1 180.88
# choose potential
-include Ta06A_pot.snap
+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
@@ -48,10 +51,9 @@ variable zblz equal 73
# Specify hybrid with SNAP, ZBL
-pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter}
-pair_style hybrid/overlay snap zbl 4 ${zblcutouter}
-pair_style hybrid/overlay snap zbl 4 4.8
-
+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
@@ -61,10 +63,11 @@ 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 gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
+SNAP keyword bzeroflag 0
+SNAP keyword quadraticflag 0
# Setup output
@@ -85,13 +88,23 @@ fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
- 2 neighbor list requests
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
-Memory usage per processor = 2.92823 Mbytes
+ 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) = 4.138 | 4.138 | 4.138 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.85157 0 -11.813095 2717.1661
10 295.96579 -11.851053 0 -11.813095 2696.1559
@@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press
80 124.04276 -11.829003 0 -11.813094 1537.703
90 97.37622 -11.825582 0 -11.813094 1734.9662
100 75.007873 -11.822714 0 -11.813094 1930.8005
-Loop time of 3.43062 on 1 procs for 100 steps with 128 atoms
+Loop time of 2.53266 on 1 procs for 100 steps with 128 atoms
-Performance: 1.259 ns/day, 19.059 hours/ns, 29.149 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 1.706 ns/day, 14.070 hours/ns, 39.484 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 3.4295 | 3.4295 | 3.4295 | 0.0 | 99.97
+Pair | 2.5313 | 2.5313 | 2.5313 | 0.0 | 99.95
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.00043988 | 0.00043988 | 0.00043988 | 0.0 | 0.01
-Output | 0.00010014 | 0.00010014 | 0.00010014 | 0.0 | 0.00
-Modify | 0.00024533 | 0.00024533 | 0.00024533 | 0.0 | 0.01
-Other | | 0.0002978 | | | 0.01
+Comm | 0.00051379 | 0.00051379 | 0.00051379 | 0.0 | 0.02
+Output | 0.00023317 | 0.00023317 | 0.00023317 | 0.0 | 0.01
+Modify | 0.00023675 | 0.00023675 | 0.00023675 | 0.0 | 0.01
+Other | | 0.0003583 | | | 0.01
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -133,4 +146,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
-Total wall time: 0:00:03
+Total wall time: 0:00:02
diff --git a/examples/snap/log.5Oct16.snap.Ta06A.g++.4 b/examples/snap/log.20Apr18.snap.Ta06A.g++.4
similarity index 71%
rename from examples/snap/log.5Oct16.snap.Ta06A.g++.4
rename to examples/snap/log.20Apr18.snap.Ta06A.g++.4
index 19d64c557c33538c702da0ddfb4fa1b30c336f8e..4d26481d5de2ccb00bbc364d70af786f458ec2e2 100644
--- a/examples/snap/log.5Oct16.snap.Ta06A.g++.4
+++ b/examples/snap/log.20Apr18.snap.Ta06A.g++.4
@@ -1,4 +1,6 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@@ -31,12 +33,13 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
+ Time spent = 0.000288486 secs
mass 1 180.88
# choose potential
-include Ta06A_pot.snap
+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
@@ -48,10 +51,9 @@ variable zblz equal 73
# Specify hybrid with SNAP, ZBL
-pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter}
-pair_style hybrid/overlay snap zbl 4 ${zblcutouter}
-pair_style hybrid/overlay snap zbl 4 4.8
-
+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
@@ -61,10 +63,11 @@ 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 gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
+SNAP keyword bzeroflag 0
+SNAP keyword quadraticflag 0
# Setup output
@@ -85,13 +88,23 @@ fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
- 2 neighbor list requests
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
-Memory usage per processor = 2.91109 Mbytes
+ 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) = 4.118 | 4.118 | 4.118 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.85157 0 -11.813095 2717.1661
10 295.8664 -11.85104 0 -11.813095 2702.935
@@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press
80 121.80051 -11.828715 0 -11.813094 1627.6911
90 95.262635 -11.825311 0 -11.813094 1812.9327
100 73.194645 -11.822481 0 -11.813094 1995.2199
-Loop time of 0.89193 on 4 procs for 100 steps with 128 atoms
+Loop time of 1.3621 on 4 procs for 100 steps with 128 atoms
-Performance: 4.843 ns/day, 4.955 hours/ns, 112.116 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 3.172 ns/day, 7.567 hours/ns, 73.416 timesteps/s
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.84444 | 0.86772 | 0.88108 | 1.6 | 97.29
+Pair | 1.2867 | 1.309 | 1.35 | 2.1 | 96.10
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.009577 | 0.023049 | 0.046417 | 9.8 | 2.58
-Output | 0.00024009 | 0.00026137 | 0.00027895 | 0.1 | 0.03
-Modify | 8.2493e-05 | 9.352e-05 | 0.00010061 | 0.1 | 0.01
-Other | | 0.0008071 | | | 0.09
+Comm | 0.0096083 | 0.050652 | 0.072999 | 10.9 | 3.72
+Output | 0.00031447 | 0.00060236 | 0.0014303 | 0.0 | 0.04
+Modify | 0.00014234 | 0.00016212 | 0.00018811 | 0.0 | 0.01
+Other | | 0.001728 | | | 0.13
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -133,4 +146,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
-Total wall time: 0:00:00
+Total wall time: 0:00:01
diff --git a/examples/snap/log.21Feb17.snap.W.2940.g++.1 b/examples/snap/log.20Apr18.snap.W.2940.g++.1
similarity index 79%
rename from examples/snap/log.21Feb17.snap.W.2940.g++.1
rename to examples/snap/log.20Apr18.snap.W.2940.g++.1
index 8c74380b8b7246dad9bf1079f17ad1ef8e56f7b8..19b2bfb40d88b1fd6dd62ab892dba1f463a48b03 100644
--- a/examples/snap/log.21Feb17.snap.W.2940.g++.1
+++ b/examples/snap/log.20Apr18.snap.W.2940.g++.1
@@ -1,4 +1,6 @@
-LAMMPS (13 Feb 2017)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
+ Time spent = 0.000190258 secs
mass 1 183.84
# choose potential
-include W_2940_2017_2.pot.snap
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+include W_2940_2017_2.snap
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
@@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
-SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
+SNAP keyword bzeroflag 0
+SNAP keyword quadraticflag 0
#Nomenclature on the snap files are Element_DakotaID_Year_Month
@@ -99,7 +103,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
-Memory usage per processor = 5.14696 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 5.15 | 5.15 | 5.15 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.028325 0 -10.98985 3010.497
10 293.40666 -11.027479 0 -10.989849 3246.0559
@@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press
80 58.605244 -10.997364 0 -10.989848 11289.914
90 39.754503 -10.994946 0 -10.989848 11824.945
100 32.524085 -10.994019 0 -10.989848 11932.118
-Loop time of 11.8271 on 1 procs for 100 steps with 128 atoms
+Loop time of 9.69738 on 1 procs for 100 steps with 128 atoms
-Performance: 0.365 ns/day, 65.706 hours/ns, 8.455 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.445 ns/day, 53.874 hours/ns, 10.312 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 11.826 | 11.826 | 11.826 | 0.0 | 99.99
+Pair | 9.6961 | 9.6961 | 9.6961 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.00044084 | 0.00044084 | 0.00044084 | 0.0 | 0.00
-Output | 0.00013232 | 0.00013232 | 0.00013232 | 0.0 | 0.00
-Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.00
-Other | | 0.0002718 | | | 0.00
+Comm | 0.00044036 | 0.00044036 | 0.00044036 | 0.0 | 0.00
+Output | 0.00024843 | 0.00024843 | 0.00024843 | 0.0 | 0.00
+Modify | 0.00023937 | 0.00023937 | 0.00023937 | 0.0 | 0.00
+Other | | 0.0003347 | | | 0.00
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -141,4 +145,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
-Total wall time: 0:00:11
+Total wall time: 0:00:09
diff --git a/examples/snap/log.21Feb17.snap.W.2940.g++.4 b/examples/snap/log.20Apr18.snap.W.2940.g++.4
similarity index 79%
rename from examples/snap/log.21Feb17.snap.W.2940.g++.4
rename to examples/snap/log.20Apr18.snap.W.2940.g++.4
index 97ed5cc8d12728a0e1d9fb2bc79729188ad7c569..dfa63fc6ea208d4552b8533a1a32fd73bc88d4fe 100644
--- a/examples/snap/log.21Feb17.snap.W.2940.g++.4
+++ b/examples/snap/log.20Apr18.snap.W.2940.g++.4
@@ -1,4 +1,6 @@
-LAMMPS (13 Feb 2017)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
+ Time spent = 0.000309944 secs
mass 1 183.84
# choose potential
-include W_2940_2017_2.pot.snap
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+include W_2940_2017_2.snap
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
@@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
-SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
+SNAP keyword bzeroflag 0
+SNAP keyword quadraticflag 0
#Nomenclature on the snap files are Element_DakotaID_Year_Month
@@ -99,7 +103,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
-Memory usage per processor = 5.12833 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 5.13 | 5.13 | 5.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.028325 0 -10.98985 3010.497
10 293.22504 -11.027456 0 -10.989849 3258.275
@@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press
80 56.127265 -10.997046 0 -10.989848 11551.687
90 38.025013 -10.994724 0 -10.989847 12069.936
100 31.768127 -10.993922 0 -10.989847 12145.648
-Loop time of 3.03545 on 4 procs for 100 steps with 128 atoms
+Loop time of 5.15615 on 4 procs for 100 steps with 128 atoms
-Performance: 1.423 ns/day, 16.864 hours/ns, 32.944 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 0.838 ns/day, 28.645 hours/ns, 19.394 timesteps/s
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 2.9594 | 2.9866 | 3.0319 | 1.6 | 98.39
+Pair | 5.0497 | 5.0762 | 5.092 | 0.8 | 98.45
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0024238 | 0.047825 | 0.075032 | 12.5 | 1.58
-Output | 0.00021601 | 0.00024045 | 0.00027442 | 0.0 | 0.01
-Modify | 9.6798e-05 | 0.00011188 | 0.00011802 | 0.0 | 0.00
-Other | | 0.000698 | | | 0.02
+Comm | 0.060802 | 0.07661 | 0.10305 | 6.1 | 1.49
+Output | 0.00040722 | 0.00078458 | 0.0018959 | 0.0 | 0.02
+Modify | 0.0002389 | 0.00024962 | 0.00027442 | 0.0 | 0.00
+Other | | 0.002315 | | | 0.04
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -141,4 +145,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
-Total wall time: 0:00:03
+Total wall time: 0:00:05
diff --git a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1
similarity index 83%
rename from examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1
rename to examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1
index 846eef269ce580ca63d730be0fb1ced38da1bf58..3f40936308b21d4e3d0ed1e8e83145c5cfd9d0f7 100644
--- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1
+++ b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1
@@ -1,4 +1,6 @@
-LAMMPS (13 Feb 2017)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
+ Time spent = 0.000431538 secs
mass 1 183.84
mass 2 4.0026
@@ -42,15 +45,15 @@ group helium type 2
5 atoms in group helium
# choose potential
-include W.SNAP_HePair.pot
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+include W_2940_2017_2_He_JW2013.snap
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL+Tabulated potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000
@@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
-SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
+SNAP keyword bzeroflag 0
+SNAP keyword quadraticflag 0
pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
Reading potential file He_He_JW2013.table with DATE: 2017-02-20
WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:476)
+ Should only be flagged at inflection points (../pair_table.cpp:481)
pair_coeff 1 2 table 2 W_He_JW2013.table WHe
Reading potential file W_He_JW2013.table with DATE: 2017-02-20
WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:476)
+ Should only be flagged at inflection points (../pair_table.cpp:481)
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
@@ -134,7 +138,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
-Memory usage per processor = 7.6729 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.676 | 7.676 | 7.676 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -10.438105 0 -10.39963 -5445.2808
10 290.48923 -10.436885 0 -10.399629 -5646.4813
@@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press
80 85.903126 -10.410645 0 -10.399628 857.74986
90 65.223651 -10.407993 0 -10.399628 1494.2746
100 59.833542 -10.407302 0 -10.399628 1938.9164
-Loop time of 11.0736 on 1 procs for 100 steps with 128 atoms
+Loop time of 8.902 on 1 procs for 100 steps with 128 atoms
-Performance: 0.390 ns/day, 61.520 hours/ns, 9.030 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.485 ns/day, 49.456 hours/ns, 11.233 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 11.072 | 11.072 | 11.072 | 0.0 | 99.99
-Neigh | 0.00041604 | 0.00041604 | 0.00041604 | 0.0 | 0.00
-Comm | 0.00046253 | 0.00046253 | 0.00046253 | 0.0 | 0.00
-Output | 0.0001657 | 0.0001657 | 0.0001657 | 0.0 | 0.00
-Modify | 0.0002265 | 0.0002265 | 0.0002265 | 0.0 | 0.00
-Other | | 0.0003119 | | | 0.00
+Pair | 8.9002 | 8.9002 | 8.9002 | 0.0 | 99.98
+Neigh | 0.00043058 | 0.00043058 | 0.00043058 | 0.0 | 0.00
+Comm | 0.00045776 | 0.00045776 | 0.00045776 | 0.0 | 0.01
+Output | 0.00025344 | 0.00025344 | 0.00025344 | 0.0 | 0.00
+Modify | 0.00022483 | 0.00022483 | 0.00022483 | 0.0 | 0.00
+Other | | 0.0003953 | | | 0.00
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156
Neighbor list builds = 1
Dangerous builds = 0
-Total wall time: 0:00:11
+Total wall time: 0:00:09
diff --git a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4
similarity index 84%
rename from examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4
rename to examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4
index 9bcbd288aa664cf29025090e8c0937e2580d905a..4ec85a63d014085449367848dbfd2c6f787a41e4 100644
--- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4
+++ b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4
@@ -1,4 +1,6 @@
-LAMMPS (13 Feb 2017)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
+ Time spent = 0.000274658 secs
mass 1 183.84
mass 2 4.0026
@@ -42,15 +45,15 @@ group helium type 2
5 atoms in group helium
# choose potential
-include W.SNAP_HePair.pot
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+include W_2940_2017_2_He_JW2013.snap
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL+Tabulated potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000
@@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
-SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
+SNAP keyword bzeroflag 0
+SNAP keyword quadraticflag 0
pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
Reading potential file He_He_JW2013.table with DATE: 2017-02-20
WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:476)
+ Should only be flagged at inflection points (../pair_table.cpp:481)
pair_coeff 1 2 table 2 W_He_JW2013.table WHe
Reading potential file W_He_JW2013.table with DATE: 2017-02-20
WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:476)
+ Should only be flagged at inflection points (../pair_table.cpp:481)
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
@@ -134,7 +138,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
-Memory usage per processor = 7.65426 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.656 | 7.656 | 7.656 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -10.438105 0 -10.39963 -5445.2808
10 292.13979 -10.437097 0 -10.39963 -5516.3963
@@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press
80 79.985938 -10.409886 0 -10.399628 2392.1106
90 62.568933 -10.407652 0 -10.399628 3141.7027
100 56.697933 -10.406899 0 -10.399628 3583.9538
-Loop time of 2.8757 on 4 procs for 100 steps with 128 atoms
+Loop time of 4.82103 on 4 procs for 100 steps with 128 atoms
-Performance: 1.502 ns/day, 15.976 hours/ns, 34.774 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 0.896 ns/day, 26.783 hours/ns, 20.742 timesteps/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 2.7363 | 2.8122 | 2.8636 | 2.9 | 97.79
+Pair | 4.4837 | 4.6734 | 4.7605 | 5.2 | 96.94
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.011014 | 0.062439 | 0.13842 | 19.3 | 2.17
-Output | 0.00023842 | 0.00025076 | 0.0002861 | 0.0 | 0.01
-Modify | 9.2506e-05 | 9.9301e-05 | 0.00010395 | 0.0 | 0.00
-Other | | 0.0006654 | | | 0.02
+Comm | 0.057389 | 0.14453 | 0.33421 | 29.4 | 3.00
+Output | 0.00038719 | 0.00073916 | 0.0017841 | 0.0 | 0.02
+Modify | 0.00018716 | 0.00022203 | 0.00026417 | 0.0 | 0.00
+Other | | 0.002119 | | | 0.04
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156
Neighbor list builds = 0
Dangerous builds = 0
-Total wall time: 0:00:02
+Total wall time: 0:00:04
diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp
index 4b114d9ce777714ee305311398421979b99f69b7..9f56cee3f1500bce3f63680e3b6fb5e398468236 100644
--- a/src/SNAP/compute_sna_atom.cpp
+++ b/src/SNAP/compute_sna_atom.cpp
@@ -276,9 +276,13 @@ void ComputeSNAAtom::compute_peratom()
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr[tid]->bvec[icoeff];
+ // diagonal element of quadratic matrix
+
+ sna[i][ncount++] = 0.5*bi*bi;
+
// upper-triangular elements of quadratic matrix
- for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++)
+ for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
sna[i][ncount++] = bi*snaptr[tid]->bvec[jcoeff];
}
}
diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp
index 54a6ce761248c3ee6fcb2c4ab14fce16e5520e00..3db0c84854f97c3d9646afacc87e7fb599fbc9f2 100644
--- a/src/SNAP/compute_snad_atom.cpp
+++ b/src/SNAP/compute_snad_atom.cpp
@@ -95,6 +95,11 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal compute snad/atom command");
rmin0 = atof(arg[iarg+1]);
iarg += 2;
+ } else if (strcmp(arg[iarg],"bzeroflag") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal compute snad/atom command");
+ bzeroflag = atoi(arg[iarg+1]);
+ iarg += 2;
} else if (strcmp(arg[iarg],"switchflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snad/atom command");
@@ -121,16 +126,11 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
}
ncoeff = snaptr[0]->ncoeff;
- twoncoeff = 2*ncoeff;
- threencoeff = 3*ncoeff;
- size_peratom_cols = threencoeff*atom->ntypes;
- if (quadraticflag) {
- ncoeffq = (ncoeff*(ncoeff+1))/2;
- twoncoeffq = 2*ncoeffq;
- threencoeffq = 3*ncoeffq;
- size_peratom_cols +=
- threencoeffq*atom->ntypes;
- }
+ nperdim = ncoeff;
+ if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
+ yoffset = nperdim;
+ zoffset = 2*nperdim;
+ size_peratom_cols = 3*nperdim*atom->ntypes;
comm_reverse = size_peratom_cols;
peratom_flag = 1;
@@ -248,9 +248,10 @@ void ComputeSNADAtom::compute_peratom()
const int* const jlist = firstneigh[i];
const int jnum = numneigh[i];
- const int typeoffset = threencoeff*(atom->type[i]-1);
- const int quadraticoffset = threencoeff*atom->ntypes +
- threencoeffq*(atom->type[i]-1);
+ // const int typeoffset = threencoeff*(atom->type[i]-1);
+ // const int quadraticoffset = threencoeff*atom->ntypes +
+ // threencoeffq*(atom->type[i]-1);
+ const int typeoffset = 3*nperdim*(atom->type[i]-1);
// insure rij, inside, and typej are of size jnum
@@ -304,16 +305,17 @@ void ComputeSNADAtom::compute_peratom()
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
snadi[icoeff] += snaptr[tid]->dbvec[icoeff][0];
- snadi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1];
- snadi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2];
+ snadi[icoeff+yoffset] += snaptr[tid]->dbvec[icoeff][1];
+ snadi[icoeff+zoffset] += snaptr[tid]->dbvec[icoeff][2];
snadj[icoeff] -= snaptr[tid]->dbvec[icoeff][0];
- snadj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1];
- snadj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2];
+ snadj[icoeff+yoffset] -= snaptr[tid]->dbvec[icoeff][1];
+ snadj[icoeff+zoffset] -= snaptr[tid]->dbvec[icoeff][2];
}
if (quadraticflag) {
- double *snadi = snad[i]+quadraticoffset;
- double *snadj = snad[j]+quadraticoffset;
+ const int quadraticoffset = ncoeff;
+ snadi += quadraticoffset;
+ snadj += quadraticoffset;
int ncount = 0;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr[tid]->bvec[icoeff];
@@ -321,21 +323,36 @@ void ComputeSNADAtom::compute_peratom()
double biy = snaptr[tid]->dbvec[icoeff][1];
double biz = snaptr[tid]->dbvec[icoeff][2];
+ // diagonal elements of quadratic matrix
+
+ double dbxtmp = bi*bix;
+ double dbytmp = bi*biy;
+ double dbztmp = bi*biz;
+
+ snadi[ncount] += dbxtmp;
+ snadi[ncount+yoffset] += dbytmp;
+ snadi[ncount+zoffset] += dbztmp;
+ snadj[ncount] -= dbxtmp;
+ snadj[ncount+yoffset] -= dbytmp;
+ snadj[ncount+zoffset] -= dbztmp;
+ ncount++;
+
// upper-triangular elements of quadratic matrix
- for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++) {
+ for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0]
+ bix*snaptr[tid]->bvec[jcoeff];
double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1]
+ biy*snaptr[tid]->bvec[jcoeff];
double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2]
+ biz*snaptr[tid]->bvec[jcoeff];
- snadi[ncount] += dbxtmp;
- snadi[ncount+ncoeffq] += dbytmp;
- snadi[ncount+twoncoeffq] += dbztmp;
- snadj[ncount] -= dbxtmp;
- snadj[ncount+ncoeffq] -= dbytmp;
- snadj[ncount+twoncoeffq] -= dbztmp;
+
+ snadi[ncount] += dbxtmp;
+ snadi[ncount+yoffset] += dbytmp;
+ snadi[ncount+zoffset] += dbztmp;
+ snadj[ncount] -= dbxtmp;
+ snadj[ncount+yoffset] -= dbytmp;
+ snadj[ncount+zoffset] -= dbztmp;
ncount++;
}
}
@@ -361,7 +378,7 @@ int ComputeSNADAtom::pack_reverse_comm(int n, int first, double *buf)
for (i = first; i < last; i++)
for (icoeff = 0; icoeff < size_peratom_cols; icoeff++)
buf[m++] = snad[i][icoeff];
- return comm_reverse;
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -387,8 +404,7 @@ double ComputeSNADAtom::memory_usage()
double bytes = nmax*size_peratom_cols * sizeof(double);
bytes += 3*njmax*sizeof(double);
bytes += njmax*sizeof(int);
- bytes += threencoeff*atom->ntypes;
- if (quadraticflag) bytes += threencoeffq*atom->ntypes;
+ bytes += 3*nperdim*atom->ntypes;
bytes += snaptr[0]->memory_usage()*comm->nthreads;
return bytes;
}
diff --git a/src/SNAP/compute_snad_atom.h b/src/SNAP/compute_snad_atom.h
index 5e40632d8c5c61f7970428ce79ed1241c794c54c..a33e6047c2c2bd0fca6d25d8a2b948fef9f7d4f9 100644
--- a/src/SNAP/compute_snad_atom.h
+++ b/src/SNAP/compute_snad_atom.h
@@ -37,7 +37,7 @@ class ComputeSNADAtom : public Compute {
private:
int nmax, njmax, diagonalstyle;
- int ncoeff, twoncoeff, threencoeff, ncoeffq, twoncoeffq, threencoeffq;
+ int ncoeff, nperdim, yoffset, zoffset;
double **cutsq;
class NeighList *list;
double **snad;
diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp
index 0278be5a97414f8dd9fb9ba681edd33255ecfbed..578f86ae5b50224d880d9ac6cebc63987f8b1ac9 100644
--- a/src/SNAP/compute_snav_atom.cpp
+++ b/src/SNAP/compute_snav_atom.cpp
@@ -96,6 +96,11 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal compute snav/atom command");
switchflag = atoi(arg[iarg+1]);
iarg += 2;
+ } else if (strcmp(arg[iarg],"bzeroflag") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal compute snav/atom command");
+ bzeroflag = atoi(arg[iarg+1]);
+ iarg += 2;
} else if (strcmp(arg[iarg],"quadraticflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snav/atom command");
@@ -117,22 +122,9 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
}
ncoeff = snaptr[0]->ncoeff;
- twoncoeff = 2*ncoeff;
- threencoeff = 3*ncoeff;
- fourncoeff = 4*ncoeff;
- fivencoeff = 5*ncoeff;
- sixncoeff = 6*ncoeff;
- size_peratom_cols = sixncoeff*atom->ntypes;
- if (quadraticflag) {
- ncoeffq = ncoeff*ncoeff;
- twoncoeffq = 2*ncoeffq;
- threencoeffq = 3*ncoeffq;
- fourncoeffq = 4*ncoeffq;
- fivencoeffq = 5*ncoeffq;
- sixncoeffq = 6*ncoeffq;
- size_peratom_cols +=
- sixncoeffq*atom->ntypes;
- }
+ nperdim = ncoeff;
+ if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
+ size_peratom_cols = 6*nperdim*atom->ntypes;
comm_reverse = size_peratom_cols;
peratom_flag = 1;
@@ -251,9 +243,7 @@ void ComputeSNAVAtom::compute_peratom()
const int* const jlist = firstneigh[i];
const int jnum = numneigh[i];
- const int typeoffset = sixncoeff*(atom->type[i]-1);
- const int quadraticoffset = sixncoeff*atom->ntypes +
- sixncoeffq*(atom->type[i]-1);
+ const int typeoffset = 6*nperdim*(atom->type[i]-1);
// insure rij, inside, and typej are of size jnum
@@ -307,23 +297,24 @@ void ComputeSNAVAtom::compute_peratom()
double *snavj = snav[j]+typeoffset;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
- snavi[icoeff] += snaptr[tid]->dbvec[icoeff][0]*xtmp;
- snavi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1]*ytmp;
- snavi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2]*ztmp;
- snavi[icoeff+threencoeff] += snaptr[tid]->dbvec[icoeff][1]*ztmp;
- snavi[icoeff+fourncoeff] += snaptr[tid]->dbvec[icoeff][0]*ztmp;
- snavi[icoeff+fivencoeff] += snaptr[tid]->dbvec[icoeff][0]*ytmp;
- snavj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][0];
- snavj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][1];
- snavj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2];
- snavj[icoeff+threencoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2];
- snavj[icoeff+fourncoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2];
- snavj[icoeff+fivencoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1];
+ snavi[icoeff] += snaptr[tid]->dbvec[icoeff][0]*xtmp;
+ snavi[icoeff+nperdim] += snaptr[tid]->dbvec[icoeff][1]*ytmp;
+ snavi[icoeff+2*nperdim] += snaptr[tid]->dbvec[icoeff][2]*ztmp;
+ snavi[icoeff+3*nperdim] += snaptr[tid]->dbvec[icoeff][1]*ztmp;
+ snavi[icoeff+4*nperdim] += snaptr[tid]->dbvec[icoeff][0]*ztmp;
+ snavi[icoeff+5*nperdim] += snaptr[tid]->dbvec[icoeff][0]*ytmp;
+ snavj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][0];
+ snavj[icoeff+nperdim] -= snaptr[tid]->dbvec[icoeff][1]*x[j][1];
+ snavj[icoeff+2*nperdim] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2];
+ snavj[icoeff+3*nperdim] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2];
+ snavj[icoeff+4*nperdim] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2];
+ snavj[icoeff+5*nperdim] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1];
}
if (quadraticflag) {
- double *snavi = snav[i]+quadraticoffset;
- double *snavj = snav[j]+quadraticoffset;
+ const int quadraticoffset = ncoeff;
+ snavi += quadraticoffset;
+ snavj += quadraticoffset;
int ncount = 0;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr[tid]->bvec[icoeff];
@@ -331,27 +322,46 @@ void ComputeSNAVAtom::compute_peratom()
double biy = snaptr[tid]->dbvec[icoeff][1];
double biz = snaptr[tid]->dbvec[icoeff][2];
+ // diagonal element of quadratic matrix
+
+ double dbxtmp = bi*bix;
+ double dbytmp = bi*biy;
+ double dbztmp = bi*biz;
+ snavi[ncount] += dbxtmp*xtmp;
+ snavi[ncount+nperdim] += dbytmp*ytmp;
+ snavi[ncount+2*nperdim] += dbztmp*ztmp;
+ snavi[ncount+3*nperdim] += dbytmp*ztmp;
+ snavi[ncount+4*nperdim] += dbxtmp*ztmp;
+ snavi[ncount+5*nperdim] += dbxtmp*ytmp;
+ snavj[ncount] -= dbxtmp*x[j][0];
+ snavj[ncount+nperdim] -= dbytmp*x[j][1];
+ snavj[ncount+2*nperdim] -= dbztmp*x[j][2];
+ snavj[ncount+3*nperdim] -= dbytmp*x[j][2];
+ snavj[ncount+4*nperdim] -= dbxtmp*x[j][2];
+ snavj[ncount+5*nperdim] -= dbxtmp*x[j][1];
+ ncount++;
+
// upper-triangular elements of quadratic matrix
- for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++) {
+ for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0]
+ bix*snaptr[tid]->bvec[jcoeff];
double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1]
+ biy*snaptr[tid]->bvec[jcoeff];
double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2]
+ biz*snaptr[tid]->bvec[jcoeff];
- snavi[ncount] += dbxtmp*xtmp;
- snavi[ncount+ncoeffq] += dbytmp*ytmp;
- snavi[ncount+twoncoeffq] += dbztmp*ztmp;
- snavi[ncount+threencoeffq] += dbytmp*ztmp;
- snavi[ncount+fourncoeffq] += dbxtmp*ztmp;
- snavi[ncount+fivencoeffq] += dbxtmp*ytmp;
- snavj[ncount] -= dbxtmp*x[j][0];
- snavj[ncount+ncoeffq] -= dbytmp*x[j][1];
- snavj[ncount+twoncoeffq] -= dbztmp*x[j][2];
- snavj[ncount+threencoeffq] -= dbytmp*x[j][2];
- snavj[ncount+fourncoeffq] -= dbxtmp*x[j][2];
- snavj[ncount+fivencoeffq] -= dbxtmp*x[j][1];
+ snavi[ncount] += dbxtmp*xtmp;
+ snavi[ncount+nperdim] += dbytmp*ytmp;
+ snavi[ncount+2*nperdim] += dbztmp*ztmp;
+ snavi[ncount+3*nperdim] += dbytmp*ztmp;
+ snavi[ncount+4*nperdim] += dbxtmp*ztmp;
+ snavi[ncount+5*nperdim] += dbxtmp*ytmp;
+ snavj[ncount] -= dbxtmp*x[j][0];
+ snavj[ncount+nperdim] -= dbytmp*x[j][1];
+ snavj[ncount+2*nperdim] -= dbztmp*x[j][2];
+ snavj[ncount+3*nperdim] -= dbytmp*x[j][2];
+ snavj[ncount+4*nperdim] -= dbxtmp*x[j][2];
+ snavj[ncount+5*nperdim] -= dbxtmp*x[j][1];
ncount++;
}
}
@@ -377,7 +387,7 @@ int ComputeSNAVAtom::pack_reverse_comm(int n, int first, double *buf)
for (i = first; i < last; i++)
for (icoeff = 0; icoeff < size_peratom_cols; icoeff++)
buf[m++] = snav[i][icoeff];
- return comm_reverse;
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -403,8 +413,8 @@ double ComputeSNAVAtom::memory_usage()
double bytes = nmax*size_peratom_cols * sizeof(double);
bytes += 3*njmax*sizeof(double);
bytes += njmax*sizeof(int);
- bytes += sixncoeff*atom->ntypes;
- if (quadraticflag) bytes += sixncoeffq*atom->ntypes;
+ bytes += 6*nperdim*atom->ntypes;
+ if (quadraticflag) bytes += 6*nperdim*atom->ntypes;
bytes += snaptr[0]->memory_usage()*comm->nthreads;
return bytes;
}
diff --git a/src/SNAP/compute_snav_atom.h b/src/SNAP/compute_snav_atom.h
index 35f1478393520dc9f2a687a0db86201b0ca5e52c..2eb9fb804f7420aab541b5995b81e39a2ca83766 100644
--- a/src/SNAP/compute_snav_atom.h
+++ b/src/SNAP/compute_snav_atom.h
@@ -37,8 +37,7 @@ class ComputeSNAVAtom : public Compute {
private:
int nmax, njmax, diagonalstyle;
- int ncoeff, twoncoeff, threencoeff, fourncoeff, fivencoeff, sixncoeff;
- int ncoeffq, twoncoeffq, threencoeffq, fourncoeffq, fivencoeffq, sixncoeffq;
+ int ncoeff, nperdim;
double **cutsq;
class NeighList *list;
double **snav;
diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp
index 377235685cd0f052d2f51ab01967a63f6679707c..8714d55c5cb3dc532056330d2a674e2aa2629089 100644
--- a/src/SNAP/pair_snap.cpp
+++ b/src/SNAP/pair_snap.cpp
@@ -278,14 +278,15 @@ void PairSNAP::compute_regular(int eflag, int vflag)
double bveci = snaptr->bvec[icoeff];
double fack = coeffi[k]*bveci;
double* dbveci = snaptr->dbvec[icoeff];
- fij[0] += fack*snaptr->dbvec[icoeff][0];
- fij[1] += fack*snaptr->dbvec[icoeff][1];
- fij[2] += fack*snaptr->dbvec[icoeff][2];
+ fij[0] += fack*dbveci[0];
+ fij[1] += fack*dbveci[1];
+ fij[2] += fack*dbveci[2];
k++;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double facki = coeffi[k]*bveci;
double fackj = coeffi[k]*snaptr->bvec[jcoeff];
double* dbvecj = snaptr->dbvec[jcoeff];
+
fij[0] += facki*dbvecj[0]+fackj*dbveci[0];
fij[1] += facki*dbvecj[1]+fackj*dbveci[1];
fij[2] += facki*dbvecj[2]+fackj*dbveci[2];
@@ -1529,10 +1530,10 @@ void PairSNAP::coeff(int narg, char **arg)
}
if (comm->me == 0)
- printf("ncoeff = %d snancoeff = %d \n",ncoeff,sna[0]->ncoeff);
- if (ncoeff != sna[0]->ncoeff) {
- error->all(FLERR,"Incorrect SNAP parameter file");
- }
+ if (ncoeff != sna[0]->ncoeff) {
+ printf("ncoeff = %d snancoeff = %d \n",ncoeff,sna[0]->ncoeff);
+ error->all(FLERR,"Incorrect SNAP parameter file");
+ }
// Calculate maximum cutoff for all elements
diff --git a/src/SNAP/pair_snap.h b/src/SNAP/pair_snap.h
index d39cb0f8d44a73b37ff5c4688b4c3f690e52f232..b60ab3c3e42657fba6fff2f316aa6e93aa5056a5 100644
--- a/src/SNAP/pair_snap.h
+++ b/src/SNAP/pair_snap.h
@@ -37,11 +37,8 @@ public:
virtual double init_one(int, int);
virtual double memory_usage();
- double rcutfac, quadraticflag; // declared public to workaround gcc 4.9
- int ncoeff; // compiler bug, manifest in KOKKOS package
-
protected:
- int ncoeffq, ncoeffall;
+ int ncoeff, ncoeffq, ncoeffall;
double **bvec, ***dbvec;
class SNA** sna;
int nmax;
@@ -100,8 +97,8 @@ protected:
double *wjelem; // elements weights
double **coeffelem; // element bispectrum coefficients
int *map; // mapping from atom types to elements
- int twojmax, diagonalstyle, switchflag, bzeroflag;
- double rfac0, rmin0, wj1, wj2;
+ int twojmax, diagonalstyle, switchflag, bzeroflag, quadraticflag;
+ double rcutfac, rfac0, rmin0, wj1, wj2;
int rcutfacflag, twojmaxflag; // flags for required parameters
};