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Merge remote-tracking branch 'upstream/develop' into compute-pace-update

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This commit is contained in:
James Michael Goff
2023-10-19 12:22:10 -06:00
parent 2ac32872e2 f641d88f86
commit ac59f47ea0
155 changed files with 4614 additions and 2097 deletions
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2
examples/mliap/in.mliap.quadratic.compute
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@ -65,7 +65,7 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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]
variable db_2_100 equal C_db[2][100]
# test output: 1: total potential energy
# 2: xy component of stress tensor

2
examples/mliap/in.mliap.snap.compute
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@ -65,7 +65,7 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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]
variable db_2_25 equal C_db[2][25]
thermo 100

12
examples/snap/in.grid.snap
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@ -67,18 +67,18 @@ compute mygridlocal all sna/grid/local grid ${ngrid} ${ngrid} ${ngrid} &
# define output
variable B5atom equal c_b[2][5]
variable B5atom equal C_b[2][5]
variable B5grid equal c_mygrid[8][8]
variable rmse_global equal "sqrt( &
(c_mygrid[8][1] - x[2])^2 + &
(c_mygrid[8][2] - y[2])^2 + &
(c_mygrid[8][3] - z[2])^2 + &
(c_mygrid[8][4] - c_b[2][1])^2 + &
(c_mygrid[8][5] - c_b[2][2])^2 + &
(c_mygrid[8][6] - c_b[2][3])^2 + &
(c_mygrid[8][7] - c_b[2][4])^2 + &
(c_mygrid[8][8] - c_b[2][5])^2 &
(c_mygrid[8][4] - C_b[2][1])^2 + &
(c_mygrid[8][5] - C_b[2][2])^2 + &
(c_mygrid[8][6] - C_b[2][3])^2 + &
(c_mygrid[8][7] - C_b[2][4])^2 + &
(c_mygrid[8][8] - C_b[2][5])^2 &
)"
thermo_style custom step v_B5atom v_B5grid v_rmse_global

12
examples/snap/in.grid.tri
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@ -87,18 +87,18 @@ compute mygridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} &
# define output
variable B5atom equal c_b[7][5]
variable B5atom equal C_b[7][5]
variable B5grid equal c_mygrid[13][8]
# do not compare x,y,z because assignment of ids
# to atoms is not unnique for different processor grids
variable rmse_global equal "sqrt( &
(c_mygrid[13][4] - c_b[7][1])^2 + &
(c_mygrid[13][5] - c_b[7][2])^2 + &
(c_mygrid[13][6] - c_b[7][3])^2 + &
(c_mygrid[13][7] - c_b[7][4])^2 + &
(c_mygrid[13][8] - c_b[7][5])^2 &
(c_mygrid[13][4] - C_b[7][1])^2 + &
(c_mygrid[13][5] - C_b[7][2])^2 + &
(c_mygrid[13][6] - C_b[7][3])^2 + &
(c_mygrid[13][7] - C_b[7][4])^2 + &
(c_mygrid[13][8] - C_b[7][5])^2 &
)"
thermo_style custom step v_B5atom v_B5grid v_rmse_global

2
examples/snap/in.snap.compute
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@ -70,7 +70,7 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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]
variable db_2_25 equal C_db[2][25]
# set up compute snap generating global array

2
examples/snap/in.snap.compute.quadratic
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@ -70,7 +70,7 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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]
variable db_2_100 equal C_db[2][100]
# set up compute snap generating global array

8
examples/voronoi/in.voronoi
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@ -146,10 +146,10 @@ variable i2 equal 257
compute v1 all voronoi/atom occupation
compute r0 all reduce sum c_v1[1]
compute r1 all reduce sum c_v1[2]
variable d5a equal c_v1[${i1}][1]
variable d5b equal c_v1[${i2}][1]
variable d5c equal c_v1[${i1}][2]
variable d5d equal c_v1[${i2}][2]
variable d5a equal C_v1[${i1}][1]
variable d5b equal C_v1[${i2}][1]
variable d5c equal C_v1[${i1}][2]
variable d5d equal C_v1[${i2}][2]
thermo_style custom c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d
run 0

11
examples/voronoi/in.voronoi.data
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@ -63,11 +63,9 @@ undump dlocal
# TEST 2:
#
# This compute voronoi generates
# local and global quantities, but
# not per-atom quantities
# This compute voronoi generates peratom and local and global quantities
compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no
compute v2 all voronoi/atom neighbors yes edge_histo 6
# write voronoi local quantities to a file
@ -75,7 +73,7 @@ dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3]
# sum up a voronoi local quantity
compute sumarea all reduce sum c_v2[3]
compute sumarea all reduce sum c_v2[3] inputs local
# output voronoi global quantities
@ -83,6 +81,3 @@ thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7]
thermo 1
run 0