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fix bug in fix wall/morse that was computing the force incorrectly

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This commit is contained in:
Axel Kohlmeyer
2023-02-23 15:20:43 -05:00
parent 2e5bc2f6b7
commit d3ac4a728d
5 changed files with 78 additions and 132 deletions
Download Patch File Download Diff File Expand all files Collapse all files

44
examples/wall/log.23Feb23.wall.lepton.g++.1
View File

@ -1,5 +1,4 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units real
atom_style bond
@ -72,7 +71,6 @@ variable name string wall-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -137,14 +135,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0
4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0
5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0
Loop time of 5.837e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 7.6828e-05 on 1 procs for 5 steps with 4 atoms
variable name string lepton-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -209,14 +206,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0
4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0
5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0
Loop time of 0.00343046 on 1 procs for 5 steps with 4 atoms
Loop time of 0.00134915 on 1 procs for 5 steps with 4 atoms
variable name string bond-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -282,14 +278,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952
4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758
5 194283.6024 91313.53086 1737.367544 25.51012833 1762.877672 12.75506417
Loop time of 6.3996e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 4.6572e-05 on 1 procs for 5 steps with 4 atoms
variable name string pair-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -354,7 +349,7 @@ Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes
3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952
4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758
5 170540.4005 97560.47089 1525.045619 190.8165235 1715.862142 178.0614593
Loop time of 5.4513e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 8.4058e-05 on 1 procs for 5 steps with 4 atoms
variable eps index 0.02
@ -363,7 +358,6 @@ variable name string wall-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -433,14 +427,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
4 178259.4975 72868.71081 1594.073105 0 1594.073105 0
5 178259.4975 72868.71081 1594.073105 0 1594.073105 0
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 5.3398e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 4.3942e-05 on 1 procs for 5 steps with 4 atoms
variable name string lepton-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -506,14 +499,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
4 178259.4975 72868.71081 1594.073105 0 1594.073105 0
5 178259.4975 72868.71081 1594.073105 0 1594.073105 0
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 0.0051554 on 1 procs for 5 steps with 4 atoms
Loop time of 0.00298781 on 1 procs for 5 steps with 4 atoms
variable name string pair-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -582,7 +574,7 @@ Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes
4 176007.6835 72778.53677 1573.936415 2.772305717 1576.708721 2.772305717
5 1.132219912e+27 4.628275436e+26 1.012479748e+25 3.761972158e+12 1.012479748e+25 3.761972158e+12
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 5.4716e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 4.4455e-05 on 1 procs for 5 steps with 4 atoms
variable d0 index 20.0
@ -593,7 +585,6 @@ variable name string wall-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -659,19 +650,18 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
Step Temp Press KinEng PotEng TotEng c_pe
0 0 0 0 -30.02905654 -30.02905654 0
1 144.4114716 59.032354 1.291389498 -31.40065042 -30.10926092 0
2 471.9742076 192.9330696 4.220596384 -34.53885647 -30.31826008 0
3 784.0772455 320.5141877 7.011556 -37.58109301 -30.56953701 0
4 961.8950756 393.2023542 8.601679525 -39.34691775 -30.74523823 0
5 996.609681 407.3929504 8.91211246 -39.66353245 -30.75141999 0
Loop time of 4.8727e-05 on 1 procs for 5 steps with 4 atoms
1 146.0893547 59.71823711 1.30639385 -31.40065042 -30.09425657 0
2 485.8091411 198.5884977 4.34431431 -34.55987817 -30.21556386 0
3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0
4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0
5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0
Loop time of 7.6505e-05 on 1 procs for 5 steps with 4 atoms
variable name string lepton-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -736,14 +726,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0
4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0
5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0
Loop time of 0.00478609 on 1 procs for 5 steps with 4 atoms
Loop time of 0.00266357 on 1 procs for 5 steps with 4 atoms
variable name string bond-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -811,14 +800,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
3 822.0828974 1456.368913 7.351418888 2.06858205 9.420000938 1.034291025
4 1018.806679 823.4383177 9.110607565 0.3120667313 9.422674297 0.1560333657
5 1050.331347 253.0262957 9.392514704 0.06784692056 9.460361624 0.03392346028
Loop time of 3.7914e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 0.000120428 on 1 procs for 5 steps with 4 atoms
variable name string pair-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -887,7 +875,7 @@ Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes
3 822.0828974 1456.368913 7.351418888 -37.63613582 -30.28471693 -18.81806791
4 1018.806679 823.4383177 9.110607565 -39.39265114 -30.28204357 -19.69632557
5 1050.331347 253.0262957 9.392514704 -39.63687095 -30.24435625 -19.81843547
Loop time of 4.2699e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 3.6356e-05 on 1 procs for 5 steps with 4 atoms
shell rm -f walltest.restart

50
examples/wall/log.23Feb23.wall.lepton.g++.4
View File

@ -1,5 +1,4 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units real
atom_style bond
@ -22,7 +21,7 @@ Created 1 atoms
create_atoms 1 single 4.0 0.0 0.0
Created 1 atoms
using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
create_atoms CPU = 0.001 seconds
create_atoms CPU = 0.000 seconds
create_atoms 1 single -5.0 0.0 0.0
Created 1 atoms
using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
@ -48,7 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
3 = max # of special neighbors
special bonds CPU = 0.000 seconds
special bonds CPU = 0.001 seconds
group move id 1:2
2 atoms in group move
@ -72,7 +71,6 @@ variable name string wall-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -137,14 +135,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0
4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0
5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0
Loop time of 0.000225045 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000266179 on 4 procs for 5 steps with 4 atoms
variable name string lepton-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -209,14 +206,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0
4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0
5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0
Loop time of 0.00491331 on 4 procs for 5 steps with 4 atoms
Loop time of 0.00230794 on 4 procs for 5 steps with 4 atoms
variable name string bond-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -282,14 +278,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952
4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758
5 194283.6024 91313.53086 1737.367544 25.51012833 1762.877672 12.75506417
Loop time of 0.000214841 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000358068 on 4 procs for 5 steps with 4 atoms
variable name string pair-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -354,7 +349,7 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.38 | 4.56 Mbytes
3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952
4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758
5 170540.4005 97560.47089 1525.045619 190.8165235 1715.862142 178.0614593
Loop time of 0.000212697 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000341881 on 4 procs for 5 steps with 4 atoms
variable eps index 0.02
@ -363,7 +358,6 @@ variable name string wall-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -433,14 +427,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
4 178259.4975 72868.71081 1594.073105 0 1594.073105 0
5 178259.4975 72868.71081 1594.073105 0 1594.073105 0
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 0.000207412 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000345376 on 4 procs for 5 steps with 4 atoms
variable name string lepton-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -506,14 +499,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
4 178259.4975 72868.71081 1594.073105 0 1594.073105 0
5 178259.4975 72868.71081 1594.073105 0 1594.073105 0
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 0.00958101 on 4 procs for 5 steps with 4 atoms
Loop time of 0.00332789 on 4 procs for 5 steps with 4 atoms
variable name string pair-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -582,7 +574,7 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.38 | 4.56 Mbytes
4 176007.6835 72778.53677 1573.936415 2.772305717 1576.708721 2.772305717
5 1.132219912e+27 4.628275436e+26 1.012479748e+25 3.761972158e+12 1.012479748e+25 3.761972158e+12
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 0.00016574 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000404238 on 4 procs for 5 steps with 4 atoms
variable d0 index 20.0
@ -593,7 +585,6 @@ variable name string wall-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -659,19 +650,18 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
Step Temp Press KinEng PotEng TotEng c_pe
0 0 0 0 -30.02905654 -30.02905654 0
1 144.4114716 59.032354 1.291389498 -31.40065042 -30.10926092 0
2 471.9742076 192.9330696 4.220596384 -34.53885647 -30.31826008 0
3 784.0772455 320.5141877 7.011556 -37.58109301 -30.56953701 0
4 961.8950756 393.2023542 8.601679525 -39.34691775 -30.74523823 0
5 996.609681 407.3929504 8.91211246 -39.66353245 -30.75141999 0
Loop time of 0.000162994 on 4 procs for 5 steps with 4 atoms
1 146.0893547 59.71823711 1.30639385 -31.40065042 -30.09425657 0
2 485.8091411 198.5884977 4.34431431 -34.55987817 -30.21556386 0
3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0
4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0
5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0
Loop time of 0.000748817 on 4 procs for 5 steps with 4 atoms
variable name string lepton-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -736,14 +726,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0
4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0
5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0
Loop time of 0.00780516 on 4 procs for 5 steps with 4 atoms
Loop time of 0.00347272 on 4 procs for 5 steps with 4 atoms
variable name string bond-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -762,7 +751,7 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
3 = max # of special neighbors
special bonds CPU = 0.000 seconds
special bonds CPU = 0.001 seconds
read_restart CPU = 0.001 seconds
# log ${name}.log
@ -811,14 +800,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
3 822.0828974 1456.368913 7.351418888 2.06858205 9.420000938 1.034291025
4 1018.806679 823.4383177 9.110607565 0.3120667313 9.422674297 0.1560333657
5 1050.331347 253.0262957 9.392514704 0.06784692056 9.460361624 0.03392346028
Loop time of 0.000141974 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000859458 on 4 procs for 5 steps with 4 atoms
variable name string pair-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -887,7 +875,7 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.38 | 4.56 Mbytes
3 822.0828974 1456.368913 7.351418888 -37.63613582 -30.28471693 -18.81806791
4 1018.806679 823.4383177 9.110607565 -39.39265114 -30.28204357 -19.69632557
5 1050.331347 253.0262957 9.392514704 -39.63687095 -30.24435625 -19.81843547
Loop time of 0.000196232 on 4 procs for 5 steps with 4 atoms
Loop time of 0.00029769 on 4 procs for 5 steps with 4 atoms
shell rm -f walltest.restart

57
examples/wall/log.23Feb23.wall.table.g++.1
View File

@ -1,5 +1,4 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units real
atom_style bond
@ -22,7 +21,7 @@ Created 1 atoms
create_atoms 1 single 4.0 0.0 0.0
Created 1 atoms
using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
create_atoms CPU = 0.000 seconds
create_atoms CPU = 0.001 seconds
create_atoms 1 single -5.0 0.0 0.0
Created 1 atoms
using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
@ -72,7 +71,6 @@ variable name string wall-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -137,14 +135,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0
4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0
5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0
Loop time of 7.7442e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 4.6507e-05 on 1 procs for 5 steps with 4 atoms
variable name string table-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -211,14 +208,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
3 115302.7492 47133.32419 1031.086781 746.8824148 1777.969196 0
4 165817.4572 67782.66799 1482.811029 285.5061521 1768.317181 0
5 194283.6024 79419.02582 1737.367544 25.51090543 1762.878449 0
Loop time of 7.9176e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 5.7549e-05 on 1 procs for 5 steps with 4 atoms
variable name string spline-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -285,14 +281,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0
4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0
5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0
Loop time of 7.4164e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 7.285e-05 on 1 procs for 5 steps with 4 atoms
variable name string bond-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -358,14 +353,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952
4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758
5 194283.6024 91313.53086 1737.367544 25.51012833 1762.877672 12.75506417
Loop time of 7.4638e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 4.5844e-05 on 1 procs for 5 steps with 4 atoms
variable name string pair-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -430,7 +424,7 @@ Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes
3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952
4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758
5 170540.4005 97560.47089 1525.045619 190.8165235 1715.862142 178.0614593
Loop time of 7.6049e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 4.6409e-05 on 1 procs for 5 steps with 4 atoms
variable eps index 0.02
@ -439,7 +433,6 @@ variable name string wall-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -509,14 +502,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
4 178259.4975 72868.71081 1594.073105 0 1594.073105 0
5 178259.4975 72868.71081 1594.073105 0 1594.073105 0
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 6.7788e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 4.3816e-05 on 1 procs for 5 steps with 4 atoms
variable name string table-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -588,14 +580,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
4 178318.0722 72892.6549 1594.596905 0 1594.596905 0
5 178318.0722 72892.6549 1594.596905 0 1594.596905 0
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 7.0625e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 4.2027e-05 on 1 procs for 5 steps with 4 atoms
variable name string spline-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -667,14 +658,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
4 162012.2554 66227.18201 1448.783278 0 1448.783278 0
5 162012.2554 66227.18201 1448.783278 0 1448.783278 0
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 7.8628e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 7.5223e-05 on 1 procs for 5 steps with 4 atoms
variable name string pair-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -743,7 +733,7 @@ Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes
4 176007.6835 72778.53677 1573.936415 2.772305717 1576.708721 2.772305717
5 1.132219912e+27 4.628275436e+26 1.012479748e+25 3.761972158e+12 1.012479748e+25 3.761972158e+12
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 5.1616e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 8.0904e-05 on 1 procs for 5 steps with 4 atoms
variable d0 index 20.0
@ -754,7 +744,6 @@ variable name string wall-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -820,19 +809,18 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
Step Temp Press KinEng PotEng TotEng c_pe
0 0 0 0 -30.02905654 -30.02905654 0
1 144.4114716 59.032354 1.291389498 -31.40065042 -30.10926092 0
2 471.9742076 192.9330696 4.220596384 -34.53885647 -30.31826008 0
3 784.0772455 320.5141877 7.011556 -37.58109301 -30.56953701 0
4 961.8950756 393.2023542 8.601679525 -39.34691775 -30.74523823 0
5 996.609681 407.3929504 8.91211246 -39.66353245 -30.75141999 0
Loop time of 3.8086e-05 on 1 procs for 5 steps with 4 atoms
1 146.0893547 59.71823711 1.30639385 -31.40065042 -30.09425657 0
2 485.8091411 198.5884977 4.34431431 -34.55987817 -30.21556386 0
3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0
4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0
5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0
Loop time of 7.721e-05 on 1 procs for 5 steps with 4 atoms
variable name string table-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -899,14 +887,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
3 822.1558136 336.0799007 7.352070936 -37.63533573 -30.28326479 0
4 1018.904947 416.5067832 9.111486314 -39.39200056 -30.28051425 0
5 1050.436268 429.3961205 9.393452958 -39.63643565 -30.24298269 0
Loop time of 3.7571e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 5.4273e-05 on 1 procs for 5 steps with 4 atoms
variable name string spline-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -973,14 +960,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
3 822.0828818 336.0500877 7.351418748 -37.63613601 -30.28471726 0
4 1018.80666 416.4666056 9.110607389 -39.39265128 -30.28204389 0
5 1050.331328 429.353223 9.392514534 -39.63687099 -30.24435645 0
Loop time of 4.1369e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 3.4052e-05 on 1 procs for 5 steps with 4 atoms
variable name string bond-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -1000,7 +986,7 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-4 neighbors
3 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_restart CPU = 0.001 seconds
read_restart CPU = 0.000 seconds
# log ${name}.log
compute ea move pe/atom
@ -1048,14 +1034,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
3 822.0828974 1456.368913 7.351418888 2.06858205 9.420000938 1.034291025
4 1018.806679 823.4383177 9.110607565 0.3120667313 9.422674297 0.1560333657
5 1050.331347 253.0262957 9.392514704 0.06784692056 9.460361624 0.03392346028
Loop time of 5.8418e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 7.2553e-05 on 1 procs for 5 steps with 4 atoms
variable name string pair-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -1124,7 +1109,7 @@ Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes
3 822.0828974 1456.368913 7.351418888 -37.63613582 -30.28471693 -18.81806791
4 1018.806679 823.4383177 9.110607565 -39.39265114 -30.28204357 -19.69632557
5 1050.331347 253.0262957 9.392514704 -39.63687095 -30.24435625 -19.81843547
Loop time of 6.2323e-05 on 1 procs for 5 steps with 4 atoms
Loop time of 4.2481e-05 on 1 procs for 5 steps with 4 atoms
shell rm -f walltest.restart

57
examples/wall/log.23Feb23.wall.table.g++.4
View File

@ -1,5 +1,4 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units real
atom_style bond
@ -48,7 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
3 = max # of special neighbors
special bonds CPU = 0.000 seconds
special bonds CPU = 0.001 seconds
group move id 1:2
2 atoms in group move
@ -72,7 +71,6 @@ variable name string wall-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -103,7 +101,7 @@ Finding 1-2 1-3 1-4 neighbors ...
special bond factors coul: 1 1 1
1 = max # of 1-2 neighbors
3 = max # of special neighbors
special bonds CPU = 0.000 seconds
special bonds CPU = 0.001 seconds
thermo_style custom step temp press ke pe etotal c_pe
thermo 1
@ -137,14 +135,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0
4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0
5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0
Loop time of 0.000226889 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000766029 on 4 procs for 5 steps with 4 atoms
variable name string table-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -211,14 +208,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
3 115302.7492 47133.32419 1031.086781 746.8824148 1777.969196 0
4 165817.4572 67782.66799 1482.811029 285.5061521 1768.317181 0
5 194283.6024 79419.02582 1737.367544 25.51090543 1762.878449 0
Loop time of 0.000222504 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000395044 on 4 procs for 5 steps with 4 atoms
variable name string spline-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -285,14 +281,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0
4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0
5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0
Loop time of 0.000211631 on 4 procs for 5 steps with 4 atoms
Loop time of 0.00033613 on 4 procs for 5 steps with 4 atoms
variable name string bond-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -358,14 +353,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952
4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758
5 194283.6024 91313.53086 1737.367544 25.51012833 1762.877672 12.75506417
Loop time of 0.00017705 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000380067 on 4 procs for 5 steps with 4 atoms
variable name string pair-harmonic
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -430,7 +424,7 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.38 | 4.56 Mbytes
3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952
4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758
5 170540.4005 97560.47089 1525.045619 190.8165235 1715.862142 178.0614593
Loop time of 0.000186388 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000337009 on 4 procs for 5 steps with 4 atoms
variable eps index 0.02
@ -439,7 +433,6 @@ variable name string wall-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -509,14 +502,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
4 178259.4975 72868.71081 1594.073105 0 1594.073105 0
5 178259.4975 72868.71081 1594.073105 0 1594.073105 0
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 0.000258277 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000404521 on 4 procs for 5 steps with 4 atoms
variable name string table-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -588,14 +580,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
4 178318.0722 72892.6549 1594.596905 0 1594.596905 0
5 178318.0722 72892.6549 1594.596905 0 1594.596905 0
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 0.000230164 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000334746 on 4 procs for 5 steps with 4 atoms
variable name string spline-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -667,14 +658,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
4 162012.2554 66227.18201 1448.783278 0 1448.783278 0
5 162012.2554 66227.18201 1448.783278 0 1448.783278 0
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 0.000182437 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000345529 on 4 procs for 5 steps with 4 atoms
variable name string pair-lj126
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -743,7 +733,7 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.38 | 4.56 Mbytes
4 176007.6835 72778.53677 1573.936415 2.772305717 1576.708721 2.772305717
5 1.132219912e+27 4.628275436e+26 1.012479748e+25 3.761972158e+12 1.012479748e+25 3.761972158e+12
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
Loop time of 0.000170205 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000315196 on 4 procs for 5 steps with 4 atoms
variable d0 index 20.0
@ -754,7 +744,6 @@ variable name string wall-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -820,19 +809,18 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
Step Temp Press KinEng PotEng TotEng c_pe
0 0 0 0 -30.02905654 -30.02905654 0
1 144.4114716 59.032354 1.291389498 -31.40065042 -30.10926092 0
2 471.9742076 192.9330696 4.220596384 -34.53885647 -30.31826008 0
3 784.0772455 320.5141877 7.011556 -37.58109301 -30.56953701 0
4 961.8950756 393.2023542 8.601679525 -39.34691775 -30.74523823 0
5 996.609681 407.3929504 8.91211246 -39.66353245 -30.75141999 0
Loop time of 0.000141964 on 4 procs for 5 steps with 4 atoms
1 146.0893547 59.71823711 1.30639385 -31.40065042 -30.09425657 0
2 485.8091411 198.5884977 4.34431431 -34.55987817 -30.21556386 0
3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0
4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0
5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0
Loop time of 0.000711295 on 4 procs for 5 steps with 4 atoms
variable name string table-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -899,14 +887,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
3 822.1558136 336.0799007 7.352070936 -37.63533573 -30.28326479 0
4 1018.904947 416.5067832 9.111486314 -39.39200056 -30.28051425 0
5 1050.436268 429.3961205 9.393452958 -39.63643565 -30.24298269 0
Loop time of 0.000146935 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000302153 on 4 procs for 5 steps with 4 atoms
variable name string spline-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -973,14 +960,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
3 822.0828818 336.0500877 7.351418748 -37.63613601 -30.28471726 0
4 1018.80666 416.4666056 9.110607389 -39.39265128 -30.28204389 0
5 1050.331328 429.353223 9.392514534 -39.63687099 -30.24435645 0
Loop time of 0.000143113 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000295181 on 4 procs for 5 steps with 4 atoms
variable name string bond-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -1048,14 +1034,13 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes
3 822.0828974 1456.368913 7.351418888 2.06858205 9.420000938 1.034291025
4 1018.806679 823.4383177 9.110607565 0.3120667313 9.422674297 0.1560333657
5 1050.331347 253.0262957 9.392514704 0.06784692056 9.460361624 0.03392346028
Loop time of 0.000130547 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000710295 on 4 procs for 5 steps with 4 atoms
variable name string pair-morse
include wall.inc
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart walltest.restart
Reading restart file ...
@ -1124,7 +1109,7 @@ Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.38 | 4.56 Mbytes
3 822.0828974 1456.368913 7.351418888 -37.63613582 -30.28471693 -18.81806791
4 1018.806679 823.4383177 9.110607565 -39.39265114 -30.28204357 -19.69632557
5 1050.331347 253.0262957 9.392514704 -39.63687095 -30.24435625 -19.81843547
Loop time of 0.000136551 on 4 procs for 5 steps with 4 atoms
Loop time of 0.000297435 on 4 procs for 5 steps with 4 atoms
shell rm -f walltest.restart

2
src/fix_wall_morse.cpp
View File

@ -71,7 +71,7 @@ void FixWallMorse::wall_particle(int m, int which, double coord)
}
double dr = delta - sigma[m];
double dexp = exp(-alpha[m] * dr);
fwall = side * coeff1[m] * (dexp * dexp - dexp) / delta;
fwall = side * coeff1[m] * (dexp * dexp - dexp);
ewall[0] += epsilon[m] * (dexp * dexp - 2.0 * dexp) - offset[m];
f[i][dim] -= fwall;
ewall[m + 1] += fwall;