2
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Why energy/pressure are slighly off, what is possible solution for making them equal. Any suggestion/comment?

clear

package gpu 1 neigh no binsize 5.0 newton off


units metal
boundary        p p p
atom_style      atomic
variable lp equal "2.86"
lattice bcc ${lp} orient x 1 0 0 orient y 0 1 0 orient z  0 0 1
region whole block 0 1 0 1 0 1 units lattice
create_box 1 whole
create_atoms 1 region whole
replicate 30 30 30
mass 1 1
# ---------- Define Interatomic Potential --------------------- 
pair_style lj/cut 2.5
pair_coeff * * 1 1

# ---------- Run Minimization --------------------- 
reset_timestep 0 
run 0

log.cpu

units metal
boundary        p p p
atom_style      atomic
variable lp equal "2.86"
lattice bcc ${lp} orient x 1 0 0 orient y 0 1 0 orient z  0 0 1
lattice bcc 2.86 orient x 1 0 0 orient y 0 1 0 orient z  0 0 1
Lattice spacing in x,y,z = 2.86 2.86 2.86
region whole block 0 1 0 1 0 1 units lattice
create_box 1 whole
Created orthogonal box = (0 0 0) to (2.86 2.86 2.86)
  1 by 1 by 2 MPI processor grid
create_atoms 1 region whole
Created 2 atoms
  using lattice units in orthogonal box = (0 0 0) to (2.86 2.86 2.86)
  create_atoms CPU = 0.000 seconds
replicate 30 30 30
Replication is creating a 30x30x30 = 27000 times larger system...
  orthogonal box = (0 0 0) to (85.8 85.8 85.8)
  1 by 1 by 2 MPI processor grid
  54000 atoms
  replicate CPU = 0.001 seconds
mass 1 1
# ---------- Define Interatomic Potential ---------------------
pair_style lj/cut 2.5
pair_coeff * * 1 1

# ---------- Run Minimization ---------------------
reset_timestep 0
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 4.5
  ghost atom cutoff = 4.5
  binsize = 2.25, bins = 39 39 39
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.22 | 10.22 | 10.22 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0             -3726.0493      0             -3726.0493     -18820.611    
Loop time of 9.615e-07 on 2 procs for 0 steps with 54000 atoms

0.0% CPU use with 2 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0          | 0          | 0          |   0.0 |  0.00
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 9.615e-07  |            |       |100.00

Nlocal:          27000 ave       27000 max       27000 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost:          14566 ave       14566 max       14566 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs:         351000 ave      351000 max      351000 min
Histogram: 2 0 0 0 0 0 0 0 0 0

Total # of neighbors = 702000
Ave neighs/atom = 13
Neighbor list builds = 0
Dangerous builds = 0



log.gpu

LAMMPS (2 Aug 2023)
Lattice spacing in x,y,z = 2.86 2.86 2.86
Created orthogonal box = (0 0 0) to (2.86 2.86 2.86)
  1 by 1 by 2 MPI processor grid
Created 2 atoms
  using lattice units in orthogonal box = (0 0 0) to (2.86 2.86 2.86)
  create_atoms CPU = 0.000 seconds
Replication is creating a 30x30x30 = 27000 times larger system...
  orthogonal box = (0 0 0) to (85.8 85.8 85.8)
  1 by 1 by 2 MPI processor grid
  54000 atoms
  replicate CPU = 0.002 seconds

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:
- GPU package (short-range, long-range and three-body potentials): doi:10.1016/j.cpc.2010.12.021, doi:10.1016/j.cpc.2011.10.012, doi:10.1016/j.cpc.2013.08.002, doi:10.1016/j.commatsci.2014.10.068, doi:10.1016/j.cpc.2016.10.020, doi:10.3233/APC200086
The log file lists these citations in BibTeX format.

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)

--------------------------------------------------------------------------
- Using acceleration for lj/cut:
-  with 2 proc(s) per device.
-  Horizontal vector operations: ENABLED
-  Shared memory system: No
--------------------------------------------------------------------------
Device 0: NVIDIA GeForce RTX 3090, 82 CUs, 17/24 GB, 1.7 GHZ (Mixed Precision)
--------------------------------------------------------------------------

Initializing Device and compiling on process 0...Done.
Initializing Device 0 on core 0...Done.
Initializing Device 0 on core 1...Done.

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 4.5
  ghost atom cutoff = 4.5
  binsize = 2.25, bins = 39 39 39
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/gpu, perpetual
      attributes: full, newton off
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Setting up Verlet run ...
  Unit style    : metal
  Current step  : 0
  Time step     : 0.001
Per MPI rank memory allocation (min/avg/max) = 13.68 | 13.68 | 13.68 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0             -3726.0488      0             -3726.0488     -18820.609    
Loop time of 1.1825e-06 on 2 procs for 0 steps with 54000 atoms

0.0% CPU use with 2 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0          | 0          | 0          |   0.0 |  0.00
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 1.183e-06  |            |       |100.00

Nlocal:          27000 ave       27000 max       27000 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost:          14566 ave       14566 max       14566 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
FullNghs:       702000 ave      702000 max      702000 min
Histogram: 2 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1404000
Ave neighs/atom = 26
Neighbor list builds = 0
Dangerous builds = 0


---------------------------------------------------------------------
      Device Time Info (average): 
---------------------------------------------------------------------
Average split:   1.0000.
Lanes / atom:    4.
Vector width:    32.
Prefetch mode:   None.
Max Mem / Proc:  7.71 MB.
CPU Cast/Pack:   0.0002 s.
CPU Driver_Time: 0.0000 s.
CPU Idle_Time:   0.0001 s.
---------------------------------------------------------------------

Total wall time: 0:00:01

output of ./lmp_gpu -h

Large-scale Atomic/Molecular Massively Parallel Simulator - 2 Aug 2023

Usage example: ./lmp_gpu -var t 300 -echo screen -in in.alloy

List of command line options supported by this LAMMPS executable:

-echo none/screen/log/both  : echoing of input script (-e)
-help                       : print this help message (-h)
-in none/filename           : read input from file or stdin (default) (-i)
-kokkos on/off ...          : turn KOKKOS mode on or off (-k)
-log none/filename          : where to send log output (-l)
-mdi '<mdi flags>'          : pass flags to the MolSSI Driver Interface
-mpicolor color             : which exe in a multi-exe mpirun cmd (-m)
-cite                       : select citation reminder style (-c)
-nocite                     : disable citation reminder (-nc)
-nonbuf                     : disable screen/logfile buffering (-nb)
-package style ...          : invoke package command (-pk)
-partition size1 size2 ...  : assign partition sizes (-p)
-plog basename              : basename for partition logs (-pl)
-pscreen basename           : basename for partition screens (-ps)
-restart2data rfile dfile ... : convert restart to data file (-r2data)
-restart2dump rfile dgroup dstyle dfile ... 
                            : convert restart to dump file (-r2dump)
-reorder topology-specs     : processor reordering (-r)
-screen none/filename       : where to send screen output (-sc)
-skiprun                    : skip loops in run and minimize (-sr)
-suffix gpu/intel/opt/omp   : style suffix to apply (-sf)
-var varname value          : set index style variable (-v)

OS: Linux "Ubuntu 22.04.2 LTS" 5.15.0-86-generic x86_64

Compiler: GNU C++ 11.4.0 with OpenMP not enabled
C++ standard: C++11
MPI v3.1: Intel(R) MPI Library 2021.6 for Linux* OS


Accelerator configuration:

GPU package API:
GPU package precision: mixed

Compatible GPU present: yes

Active compile time flags:

-DLAMMPS_GZIP
-DLAMMPS_SMALLBIG
sizeof(smallint): 32-bit
sizeof(imageint): 32-bit
sizeof(tagint):   32-bit
sizeof(bigint):   64-bit

Available compression formats:

Extension: .gz     Command: gzip
Extension: .bz2    Command: bzip2
Extension: .zst    Command: zstd
Extension: .xz     Command: xz
Extension: .lzma   Command: xz
Extension: .lz4    Command: lz4


Installed packages:

GPU MANYBODY MEAM REPLICA 
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2
  • $\begingroup$ What happens if you run the same system with multiple replicas? It is expected that running several time you obtain different values. $\endgroup$
    – Camps
    Commented Oct 18, 2023 at 13:49
  • $\begingroup$ @Camps no values remained constant. It is static calculation with frozen atoms, just calculating energy by summing pairwise interactions . $\endgroup$ Commented Oct 18, 2023 at 13:53

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