add simple general triclinic example files
This commit is contained in:
Steve Plimpton
110
examples/triclinic/README
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110
examples/triclinic/README
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* Various input scripts for systems with general triclinic boxes
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versus orthogonal boxes
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in.bcc.primitive = 1 atom for bcc lattice with primitive unit cell
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in.fcc.primitive = 1 atom for fcc lattice with primitive unit cell
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in.hex.primitive = 1 atom for 2d hex lattice with primitive unit cell
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in.sq2.primitive = 1 atom for 2d sq2 lattice with primitive unit cell
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in.bcc.orthog = 2 atoms for bcc lattice with orthogonal unit cell
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in.fcc.orthog = 4 atoms for fcc lattice with orthogonal unit cell
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in.hex.orthog = 2 atoms for 2d hex ;attice with orthogonal unit cell
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in.sq2.orthog = 2 atoms for 2d sq2 lattice with orthogonal unit cell
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energy and pressure should be same for primitive and orthogonal unit cells
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in.data.general = read a data file in general triclinic format
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* Run all the scripts on 1 proc
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lmp_mpi < in.bcc.primitive
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mv log.lammps log.compare.bcc.primitive.g++.1
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mv tmp.data.bcc.primitive data.compare.bcc.primitive.g++.1
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mv tmp.dump.bcc.primitive dump.compare.bcc.primitive.g++.1
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lmp_mpi < in.fcc.primitive
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mv log.lammps log.compare.fcc.primitive.g++.1
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mv tmp.data.fcc.primitive data.compare.fcc.primitive.g++.1
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mv tmp.dump.fcc.primitive dump.compare.fcc.primitive.g++.1
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lmp_mpi < in.hex.primitive
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mv log.lammps log.compare.hex.primitive.g++.1
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mv tmp.data.hex.primitive data.compare.hex.primitive.g++.1
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mv tmp.dump.hex.primitive dump.compare.hex.primitive.g++.1
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lmp_mpi < in.sq2.primitive
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mv log.lammps log.compare.sq2.primitive.g++.1
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mv tmp.data.sq2.primitive data.compare.sq2.primitive.g++.1
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mv tmp.dump.sq2.primitive dump.compare.sq2.primitive.g++.1
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lmp_mpi < in.bcc.orthog
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mv log.lammps log.compare.bcc.orthog.g++.1
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mv tmp.data.bcc.orthog data.compare.bcc.orthog.g++.1
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mv tmp.dump.bcc.orthog dump.compare.bcc.orthog.g++.1
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lmp_mpi < in.fcc.orthog
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mv log.lammps log.compare.fcc.orthog.g++.1
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mv tmp.data.fcc.orthog data.compare.fcc.orthog.g++.1
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mv tmp.dump.fcc.orthog dump.compare.fcc.orthog.g++.1
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lmp_mpi < in.hex.orthog
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mv log.lammps log.compare.hex.orthog.g++.1
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mv tmp.data.hex.orthog data.compare.hex.orthog.g++.1
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mv tmp.dump.hex.orthog dump.compare.hex.orthog.g++.1
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lmp_mpi < in.sq2.orthog
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mv log.lammps log.compare.sq2.orthog.g++.1
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mv tmp.data.sq2.orthog data.compare.sq2.orthog.g++.1
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mv tmp.dump.sq2.orthog dump.compare.sq2.orthog.g++.1
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lmp_mpi < in.data.general
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mv log.lammps log.compare.data.general.g++.1
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mv tmp.data.general data.compare.general.g++.1
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mv tmp.dump.general dump.compare.general.g++.1
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* Run all the scripts on 4 procs
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mpirun -np 4 lmp_mpi < in.bcc.primitive
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mv log.lammps log.compare.bcc.primitive.g++.4
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mv tmp.data.bcc.primitive data.compare.bcc.primitive.g++.4
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mv tmp.dump.bcc.primitive dump.compare.bcc.primitive.g++.4
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mpirun -np 4 lmp_mpi < in.fcc.primitive
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mv log.lammps log.compare.fcc.primitive.g++.4
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mv tmp.data.fcc.primitive data.compare.fcc.primitive.g++.4
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mv tmp.dump.fcc.primitive dump.compare.fcc.primitive.g++.4
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mpirun -np 4 lmp_mpi < in.hex.primitive
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mv log.lammps log.compare.hex.primitive.g++.4
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mv tmp.data.hex.primitive data.compare.hex.primitive.g++.4
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mv tmp.dump.hex.primitive dump.compare.hex.primitive.g++.4
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mpirun -np 4 lmp_mpi < in.sq2.primitive
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mv log.lammps log.compare.sq2.primitive.g++.4
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mv tmp.data.sq2.primitive data.compare.sq2.primitive.g++.4
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mv tmp.dump.sq2.primitive dump.compare.sq2.primitive.g++.4
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mpirun -np 4 lmp_mpi < in.bcc.orthog
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mv log.lammps log.compare.bcc.orthog.g++.4
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mv tmp.data.bcc.orthog data.compare.bcc.orthog.g++.4
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mv tmp.dump.bcc.orthog dump.compare.bcc.orthog.g++.4
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mpirun -np 4 lmp_mpi < in.fcc.orthog
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mv log.lammps log.compare.fcc.orthog.g++.4
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mv tmp.data.fcc.orthog data.compare.fcc.orthog.g++.4
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mv tmp.dump.fcc.orthog dump.compare.fcc.orthog.g++.4
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mpirun -np 4 lmp_mpi < in.hex.orthog
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mv log.lammps log.compare.hex.orthog.g++.4
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mv tmp.data.hex.orthog data.compare.hex.orthog.g++.4
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mv tmp.dump.hex.orthog dump.compare.hex.orthog.g++.4
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mpirun -np 4 lmp_mpi < in.sq2.orthog
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mv log.lammps log.compare.sq2.orthog.g++.4
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mv tmp.data.sq2.orthog data.compare.sq2.orthog.g++.4
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mv tmp.dump.sq2.orthog dump.compare.sq2.orthog.g++.4
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mpirun -np 4 lmp_mpi < in.data.general
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mv log.lammps log.compare.data.general.g++.4
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mv tmp.data.general data.compare.general.g++.4
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mv tmp.dump.general dump.compare.general.g++.4
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22
examples/triclinic/data.8Apr24.bcc.orthog.g++.1
Normal file
22
examples/triclinic/data.8Apr24.bcc.orthog.g++.1
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LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
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2 atoms
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1 atom types
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0 1.2599210498948732 xlo xhi
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0 1.2599210498948732 ylo yhi
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0 1.2599210498948732 zlo zhi
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Masses
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1 1
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Atoms # atomic
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1 1 0 0 0 0 0 0
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2 1 0.6299605249474366 0.6299605249474366 0.6299605249474366 0 0 0
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Velocities
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1 0 0 0
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2 0 0 0
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22
examples/triclinic/data.8Apr24.bcc.orthog.g++.4
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22
examples/triclinic/data.8Apr24.bcc.orthog.g++.4
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LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
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2 atoms
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1 atom types
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0 1.2599210498948732 xlo xhi
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0 1.2599210498948732 ylo yhi
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0 1.2599210498948732 zlo zhi
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Masses
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1 1
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Atoms # atomic
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1 1 0 0 0 0 0 0
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2 1 0.6299605249474366 0.6299605249474366 0.6299605249474366 0 0 0
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Velocities
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1 0 0 0
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2 0 0 0
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21
examples/triclinic/data.8Apr24.bcc.primitive.g++.1
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21
examples/triclinic/data.8Apr24.bcc.primitive.g++.1
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LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
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1 atoms
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1 atom types
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-0.6299605249474365 0.6299605249474365 0.6299605249474364 avec
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0.6299605249474367 -0.6299605249474365 0.6299605249474365 bvec
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0.6299605249474363 0.6299605249474365 -0.6299605249474363 cvec
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0 0 0 abc origin
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Masses
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1 1
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Atoms # atomic
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1 1 0 0 0 0 0 0
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Velocities
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1 0 0 0
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21
examples/triclinic/data.8Apr24.bcc.primitive.g++.4
Normal file
21
examples/triclinic/data.8Apr24.bcc.primitive.g++.4
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@ -0,0 +1,21 @@
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LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
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1 atoms
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1 atom types
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-0.6299605249474365 0.6299605249474365 0.6299605249474364 avec
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0.6299605249474367 -0.6299605249474365 0.6299605249474365 bvec
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0.6299605249474363 0.6299605249474365 -0.6299605249474363 cvec
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0 0 0 abc origin
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Masses
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1 1
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Atoms # atomic
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1 1 0 0 0 0 0 0
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Velocities
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1 0 0 0
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26
examples/triclinic/data.8Apr24.fcc.orthog.g++.1
Normal file
26
examples/triclinic/data.8Apr24.fcc.orthog.g++.1
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@ -0,0 +1,26 @@
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LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
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4 atoms
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1 atom types
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0 1.5377619196572583 xlo xhi
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0 1.5377619196572583 ylo yhi
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0 1.5377619196572583 zlo zhi
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Masses
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1 1
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Atoms # atomic
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1 1 0 0 0 0 0 0
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2 1 0.7688809598286291 0.7688809598286291 0 0 0 0
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3 1 0.7688809598286291 0 0.7688809598286291 0 0 0
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4 1 0 0.7688809598286291 0.7688809598286291 0 0 0
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Velocities
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1 0 0 0
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2 0 0 0
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3 0 0 0
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4 0 0 0
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26
examples/triclinic/data.8Apr24.fcc.orthog.g++.4
Normal file
26
examples/triclinic/data.8Apr24.fcc.orthog.g++.4
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@ -0,0 +1,26 @@
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LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
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4 atoms
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1 atom types
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0 1.5377619196572583 xlo xhi
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0 1.5377619196572583 ylo yhi
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0 1.5377619196572583 zlo zhi
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Masses
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1 1
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Atoms # atomic
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1 1 0 0 0 0 0 0
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2 1 0 0.7688809598286291 0.7688809598286291 0 0 0
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3 1 0.7688809598286291 0.7688809598286291 0 0 0 0
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4 1 0.7688809598286291 0 0.7688809598286291 0 0 0
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Velocities
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1 0 0 0
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2 0 0 0
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3 0 0 0
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4 0 0 0
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21
examples/triclinic/data.8Apr24.fcc.primitive.g++.1
Normal file
21
examples/triclinic/data.8Apr24.fcc.primitive.g++.1
Normal file
@ -0,0 +1,21 @@
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LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
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1 atoms
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1 atom types
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0.7688809598286291 0.7688809598286293 -6.036070983262366e-17 avec
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-5.551115123125783e-17 0.7688809598286293 0.7688809598286293 bvec
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0.768880959828629 0 0.768880959828629 cvec
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0 0 0 abc origin
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Masses
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1 1
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Atoms # atomic
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1 1 0 0 0 0 0 0
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Velocities
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1 0 0 0
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21
examples/triclinic/data.8Apr24.fcc.primitive.g++.4
Normal file
21
examples/triclinic/data.8Apr24.fcc.primitive.g++.4
Normal file
@ -0,0 +1,21 @@
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LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
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1 atoms
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1 atom types
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0.7688809598286291 0.7688809598286293 -6.036070983262366e-17 avec
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-5.551115123125783e-17 0.7688809598286293 0.7688809598286293 bvec
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0.768880959828629 0 0.768880959828629 cvec
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0 0 0 abc origin
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Masses
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1 1
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Atoms # atomic
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1 1 0 0 0 0 0 0
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Velocities
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1 0 0 0
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23
examples/triclinic/data.8Apr24.general.g++.1
Normal file
23
examples/triclinic/data.8Apr24.general.g++.1
Normal file
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LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
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2 atoms
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1 atom types
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0.9999999999999998 -1 0 avec
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0.9999999999999999 0.9999999999999999 0 bvec
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0.9999999999999999 0.9999999999999999 1 cvec
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0 0 0 abc origin
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Masses
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1 1
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Atoms # atomic
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1 1 0.2 -1.3877787807814457e-17 0.1 0 0 0
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2 1 0.8 -1.1102230246251565e-16 0.3 0 0 0
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Velocities
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1 0 0 0
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2 0 0 0
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23
examples/triclinic/data.8Apr24.general.g++.4
Normal file
23
examples/triclinic/data.8Apr24.general.g++.4
Normal file
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LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
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2 atoms
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1 atom types
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0.9999999999999998 -1 0 avec
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0.9999999999999999 0.9999999999999999 0 bvec
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0.9999999999999999 0.9999999999999999 1 cvec
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0 0 0 abc origin
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Masses
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1 1
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Atoms # atomic
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1 1 0.2 -1.3877787807814457e-17 0.1 0 0 0
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2 1 0.8 -1.1102230246251565e-16 0.3 0 0 0
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Velocities
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1 0 0 0
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2 0 0 0
|
||||||
22
examples/triclinic/data.8Apr24.hex.orthog.g++.1
Normal file
22
examples/triclinic/data.8Apr24.hex.orthog.g++.1
Normal file
@ -0,0 +1,22 @@
|
|||||||
|
LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
|
||||||
|
|
||||||
|
2 atoms
|
||||||
|
1 atom types
|
||||||
|
|
||||||
|
0 1.074569931823542 xlo xhi
|
||||||
|
0 1.8612097182041991 ylo yhi
|
||||||
|
-0.537284965911771 0.537284965911771 zlo zhi
|
||||||
|
|
||||||
|
Masses
|
||||||
|
|
||||||
|
1 1
|
||||||
|
|
||||||
|
Atoms # atomic
|
||||||
|
|
||||||
|
1 1 0 0 0 0 0 0
|
||||||
|
2 1 0.537284965911771 0.9306048591020996 0 0 0 0
|
||||||
|
|
||||||
|
Velocities
|
||||||
|
|
||||||
|
1 0 0 0
|
||||||
|
2 0 0 0
|
||||||
22
examples/triclinic/data.8Apr24.hex.orthog.g++.4
Normal file
22
examples/triclinic/data.8Apr24.hex.orthog.g++.4
Normal file
@ -0,0 +1,22 @@
|
|||||||
|
LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
|
||||||
|
|
||||||
|
2 atoms
|
||||||
|
1 atom types
|
||||||
|
|
||||||
|
0 1.074569931823542 xlo xhi
|
||||||
|
0 1.8612097182041991 ylo yhi
|
||||||
|
-0.537284965911771 0.537284965911771 zlo zhi
|
||||||
|
|
||||||
|
Masses
|
||||||
|
|
||||||
|
1 1
|
||||||
|
|
||||||
|
Atoms # atomic
|
||||||
|
|
||||||
|
1 1 0 0 0 0 0 0
|
||||||
|
2 1 0.537284965911771 0.9306048591020996 0 0 0 0
|
||||||
|
|
||||||
|
Velocities
|
||||||
|
|
||||||
|
1 0 0 0
|
||||||
|
2 0 0 0
|
||||||
21
examples/triclinic/data.8Apr24.hex.primitive.g++.1
Normal file
21
examples/triclinic/data.8Apr24.hex.primitive.g++.1
Normal file
@ -0,0 +1,21 @@
|
|||||||
|
LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
|
||||||
|
|
||||||
|
1 atoms
|
||||||
|
1 atom types
|
||||||
|
|
||||||
|
1.0745699318262956 0 0 avec
|
||||||
|
0.5372849659131478 0.9306048590997147 0 bvec
|
||||||
|
0 0 1.0745699318262956 cvec
|
||||||
|
0 0 -0.5372849659131478 abc origin
|
||||||
|
|
||||||
|
Masses
|
||||||
|
|
||||||
|
1 1
|
||||||
|
|
||||||
|
Atoms # atomic
|
||||||
|
|
||||||
|
1 1 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Velocities
|
||||||
|
|
||||||
|
1 0 0 0
|
||||||
21
examples/triclinic/data.8Apr24.hex.primitive.g++.4
Normal file
21
examples/triclinic/data.8Apr24.hex.primitive.g++.4
Normal file
@ -0,0 +1,21 @@
|
|||||||
|
LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
|
||||||
|
|
||||||
|
1 atoms
|
||||||
|
1 atom types
|
||||||
|
|
||||||
|
1.0745699318262956 0 0 avec
|
||||||
|
0.5372849659131478 0.9306048590997147 0 bvec
|
||||||
|
0 0 1.0745699318262956 cvec
|
||||||
|
0 0 -0.5372849659131478 abc origin
|
||||||
|
|
||||||
|
Masses
|
||||||
|
|
||||||
|
1 1
|
||||||
|
|
||||||
|
Atoms # atomic
|
||||||
|
|
||||||
|
1 1 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Velocities
|
||||||
|
|
||||||
|
1 0 0 0
|
||||||
22
examples/triclinic/data.8Apr24.sq2.orthog.g++.1
Normal file
22
examples/triclinic/data.8Apr24.sq2.orthog.g++.1
Normal file
@ -0,0 +1,22 @@
|
|||||||
|
LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
|
||||||
|
|
||||||
|
2 atoms
|
||||||
|
1 atom types
|
||||||
|
|
||||||
|
0 1.348399724926484 xlo xhi
|
||||||
|
0 1.348399724926484 ylo yhi
|
||||||
|
-0.674199862463242 0.674199862463242 zlo zhi
|
||||||
|
|
||||||
|
Masses
|
||||||
|
|
||||||
|
1 1
|
||||||
|
|
||||||
|
Atoms # atomic
|
||||||
|
|
||||||
|
1 1 0 0 0 0 0 0
|
||||||
|
2 1 0.674199862463242 0.674199862463242 0 0 0 0
|
||||||
|
|
||||||
|
Velocities
|
||||||
|
|
||||||
|
1 0 0 0
|
||||||
|
2 0 0 0
|
||||||
22
examples/triclinic/data.8Apr24.sq2.orthog.g++.4
Normal file
22
examples/triclinic/data.8Apr24.sq2.orthog.g++.4
Normal file
@ -0,0 +1,22 @@
|
|||||||
|
LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
|
||||||
|
|
||||||
|
2 atoms
|
||||||
|
1 atom types
|
||||||
|
|
||||||
|
0 1.348399724926484 xlo xhi
|
||||||
|
0 1.348399724926484 ylo yhi
|
||||||
|
-0.674199862463242 0.674199862463242 zlo zhi
|
||||||
|
|
||||||
|
Masses
|
||||||
|
|
||||||
|
1 1
|
||||||
|
|
||||||
|
Atoms # atomic
|
||||||
|
|
||||||
|
1 1 0 0 0 0 0 0
|
||||||
|
2 1 0.674199862463242 0.674199862463242 0 0 0 0
|
||||||
|
|
||||||
|
Velocities
|
||||||
|
|
||||||
|
1 0 0 0
|
||||||
|
2 0 0 0
|
||||||
21
examples/triclinic/data.8Apr24.sq2.primitive.g++.1
Normal file
21
examples/triclinic/data.8Apr24.sq2.primitive.g++.1
Normal file
@ -0,0 +1,21 @@
|
|||||||
|
LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
|
||||||
|
|
||||||
|
1 atoms
|
||||||
|
1 atom types
|
||||||
|
|
||||||
|
0.6741998624632419 -0.674199862463242 0 avec
|
||||||
|
0.6741998624632419 0.674199862463242 0 bvec
|
||||||
|
0 0 1.348399724926484 cvec
|
||||||
|
0 0 -0.674199862463242 abc origin
|
||||||
|
|
||||||
|
Masses
|
||||||
|
|
||||||
|
1 1
|
||||||
|
|
||||||
|
Atoms # atomic
|
||||||
|
|
||||||
|
1 1 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Velocities
|
||||||
|
|
||||||
|
1 0 0 0
|
||||||
21
examples/triclinic/data.8Apr24.sq2.primitive.g++.4
Normal file
21
examples/triclinic/data.8Apr24.sq2.primitive.g++.4
Normal file
@ -0,0 +1,21 @@
|
|||||||
|
LAMMPS data file via write_data, version 7 Feb 2024, timestep = 0, units = lj
|
||||||
|
|
||||||
|
1 atoms
|
||||||
|
1 atom types
|
||||||
|
|
||||||
|
0.6741998624632419 -0.674199862463242 0 avec
|
||||||
|
0.6741998624632419 0.674199862463242 0 bvec
|
||||||
|
0 0 1.348399724926484 cvec
|
||||||
|
0 0 -0.674199862463242 abc origin
|
||||||
|
|
||||||
|
Masses
|
||||||
|
|
||||||
|
1 1
|
||||||
|
|
||||||
|
Atoms # atomic
|
||||||
|
|
||||||
|
1 1 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Velocities
|
||||||
|
|
||||||
|
1 0 0 0
|
||||||
13
examples/triclinic/data.general
Normal file
13
examples/triclinic/data.general
Normal file
@ -0,0 +1,13 @@
|
|||||||
|
# simple general triclinic simulation box with 2 atoms
|
||||||
|
|
||||||
|
2 atoms
|
||||||
|
1 atom types
|
||||||
|
1 -1 0 avec
|
||||||
|
1 1 0 bvec
|
||||||
|
1 1 1 cvec
|
||||||
|
0 0 0 abc origin
|
||||||
|
|
||||||
|
Atoms
|
||||||
|
|
||||||
|
1 1 0.2 0.0 0.1
|
||||||
|
2 1 0.8 0.0 0.3
|
||||||
11
examples/triclinic/dump.8Apr24.bcc.orthog.g++.1
Normal file
11
examples/triclinic/dump.8Apr24.bcc.orthog.g++.1
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
2
|
||||||
|
ITEM: BOX BOUNDS pp pp pp
|
||||||
|
0.0000000000000000e+00 1.2599210498948732e+00
|
||||||
|
0.0000000000000000e+00 1.2599210498948732e+00
|
||||||
|
0.0000000000000000e+00 1.2599210498948732e+00
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
|
2 1 0.629961 0.629961 0.629961
|
||||||
11
examples/triclinic/dump.8Apr24.bcc.orthog.g++.4
Normal file
11
examples/triclinic/dump.8Apr24.bcc.orthog.g++.4
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
2
|
||||||
|
ITEM: BOX BOUNDS pp pp pp
|
||||||
|
0.0000000000000000e+00 1.2599210498948732e+00
|
||||||
|
0.0000000000000000e+00 1.2599210498948732e+00
|
||||||
|
0.0000000000000000e+00 1.2599210498948732e+00
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
|
2 1 0.629961 0.629961 0.629961
|
||||||
10
examples/triclinic/dump.8Apr24.bcc.primitive.g++.1
Normal file
10
examples/triclinic/dump.8Apr24.bcc.primitive.g++.1
Normal file
@ -0,0 +1,10 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
1
|
||||||
|
ITEM: BOX BOUNDS abc origin pp pp pp
|
||||||
|
-6.2996052494743648e-01 6.2996052494743648e-01 6.2996052494743637e-01 0.0000000000000000e+00
|
||||||
|
6.2996052494743671e-01 -6.2996052494743648e-01 6.2996052494743648e-01 0.0000000000000000e+00
|
||||||
|
6.2996052494743626e-01 6.2996052494743648e-01 -6.2996052494743626e-01 0.0000000000000000e+00
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
10
examples/triclinic/dump.8Apr24.bcc.primitive.g++.4
Normal file
10
examples/triclinic/dump.8Apr24.bcc.primitive.g++.4
Normal file
@ -0,0 +1,10 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
1
|
||||||
|
ITEM: BOX BOUNDS abc origin pp pp pp
|
||||||
|
-6.2996052494743648e-01 6.2996052494743648e-01 6.2996052494743637e-01 0.0000000000000000e+00
|
||||||
|
6.2996052494743671e-01 -6.2996052494743648e-01 6.2996052494743648e-01 0.0000000000000000e+00
|
||||||
|
6.2996052494743626e-01 6.2996052494743648e-01 -6.2996052494743626e-01 0.0000000000000000e+00
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
13
examples/triclinic/dump.8Apr24.fcc.orthog.g++.1
Normal file
13
examples/triclinic/dump.8Apr24.fcc.orthog.g++.1
Normal file
@ -0,0 +1,13 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
4
|
||||||
|
ITEM: BOX BOUNDS pp pp pp
|
||||||
|
0.0000000000000000e+00 1.5377619196572583e+00
|
||||||
|
0.0000000000000000e+00 1.5377619196572583e+00
|
||||||
|
0.0000000000000000e+00 1.5377619196572583e+00
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
|
2 1 0.768881 0.768881 0
|
||||||
|
3 1 0.768881 0 0.768881
|
||||||
|
4 1 0 0.768881 0.768881
|
||||||
13
examples/triclinic/dump.8Apr24.fcc.orthog.g++.4
Normal file
13
examples/triclinic/dump.8Apr24.fcc.orthog.g++.4
Normal file
@ -0,0 +1,13 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
4
|
||||||
|
ITEM: BOX BOUNDS pp pp pp
|
||||||
|
0.0000000000000000e+00 1.5377619196572583e+00
|
||||||
|
0.0000000000000000e+00 1.5377619196572583e+00
|
||||||
|
0.0000000000000000e+00 1.5377619196572583e+00
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
|
2 1 0 0.768881 0.768881
|
||||||
|
3 1 0.768881 0.768881 0
|
||||||
|
4 1 0.768881 0 0.768881
|
||||||
10
examples/triclinic/dump.8Apr24.fcc.primitive.g++.1
Normal file
10
examples/triclinic/dump.8Apr24.fcc.primitive.g++.1
Normal file
@ -0,0 +1,10 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
1
|
||||||
|
ITEM: BOX BOUNDS abc origin pp pp pp
|
||||||
|
7.6888095982862914e-01 7.6888095982862925e-01 -6.0360709832623663e-17 0.0000000000000000e+00
|
||||||
|
-5.5511151231257827e-17 7.6888095982862925e-01 7.6888095982862925e-01 0.0000000000000000e+00
|
||||||
|
7.6888095982862903e-01 0.0000000000000000e+00 7.6888095982862903e-01 0.0000000000000000e+00
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
10
examples/triclinic/dump.8Apr24.fcc.primitive.g++.4
Normal file
10
examples/triclinic/dump.8Apr24.fcc.primitive.g++.4
Normal file
@ -0,0 +1,10 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
1
|
||||||
|
ITEM: BOX BOUNDS abc origin pp pp pp
|
||||||
|
7.6888095982862914e-01 7.6888095982862925e-01 -6.0360709832623663e-17 0.0000000000000000e+00
|
||||||
|
-5.5511151231257827e-17 7.6888095982862925e-01 7.6888095982862925e-01 0.0000000000000000e+00
|
||||||
|
7.6888095982862903e-01 0.0000000000000000e+00 7.6888095982862903e-01 0.0000000000000000e+00
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
11
examples/triclinic/dump.8Apr24.general.g++.1
Normal file
11
examples/triclinic/dump.8Apr24.general.g++.1
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
2
|
||||||
|
ITEM: BOX BOUNDS abc origin pp pp pp
|
||||||
|
9.9999999999999978e-01 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
9.9999999999999989e-01 9.9999999999999989e-01 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
9.9999999999999989e-01 9.9999999999999989e-01 1.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0.141421 0.141421 0.1
|
||||||
|
2 1 0.565685 0.565685 0.3
|
||||||
11
examples/triclinic/dump.8Apr24.general.g++.4
Normal file
11
examples/triclinic/dump.8Apr24.general.g++.4
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
2
|
||||||
|
ITEM: BOX BOUNDS abc origin pp pp pp
|
||||||
|
9.9999999999999978e-01 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
9.9999999999999989e-01 9.9999999999999989e-01 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
9.9999999999999989e-01 9.9999999999999989e-01 1.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0.141421 0.141421 0.1
|
||||||
|
2 1 0.565685 0.565685 0.3
|
||||||
11
examples/triclinic/dump.8Apr24.hex.orthog.g++.1
Normal file
11
examples/triclinic/dump.8Apr24.hex.orthog.g++.1
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
2
|
||||||
|
ITEM: BOX BOUNDS pp pp pp
|
||||||
|
0.0000000000000000e+00 1.0745699318235420e+00
|
||||||
|
0.0000000000000000e+00 1.8612097182041991e+00
|
||||||
|
-5.3728496591177100e-01 5.3728496591177100e-01
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
|
2 1 0.537285 0.930605 0
|
||||||
11
examples/triclinic/dump.8Apr24.hex.orthog.g++.4
Normal file
11
examples/triclinic/dump.8Apr24.hex.orthog.g++.4
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
2
|
||||||
|
ITEM: BOX BOUNDS pp pp pp
|
||||||
|
0.0000000000000000e+00 1.0745699318235420e+00
|
||||||
|
0.0000000000000000e+00 1.8612097182041991e+00
|
||||||
|
-5.3728496591177100e-01 5.3728496591177100e-01
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
|
2 1 0.537285 0.930605 0
|
||||||
10
examples/triclinic/dump.8Apr24.hex.primitive.g++.1
Normal file
10
examples/triclinic/dump.8Apr24.hex.primitive.g++.1
Normal file
@ -0,0 +1,10 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
1
|
||||||
|
ITEM: BOX BOUNDS abc origin pp pp pp
|
||||||
|
1.0745699318262956e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
5.3728496591314778e-01 9.3060485909971469e-01 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
0.0000000000000000e+00 0.0000000000000000e+00 1.0745699318262956e+00 -5.3728496591314778e-01
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
10
examples/triclinic/dump.8Apr24.hex.primitive.g++.4
Normal file
10
examples/triclinic/dump.8Apr24.hex.primitive.g++.4
Normal file
@ -0,0 +1,10 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
1
|
||||||
|
ITEM: BOX BOUNDS abc origin pp pp pp
|
||||||
|
1.0745699318262956e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
5.3728496591314778e-01 9.3060485909971469e-01 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
0.0000000000000000e+00 0.0000000000000000e+00 1.0745699318262956e+00 -5.3728496591314778e-01
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
11
examples/triclinic/dump.8Apr24.sq2.orthog.g++.1
Normal file
11
examples/triclinic/dump.8Apr24.sq2.orthog.g++.1
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
2
|
||||||
|
ITEM: BOX BOUNDS pp pp pp
|
||||||
|
0.0000000000000000e+00 1.3483997249264841e+00
|
||||||
|
0.0000000000000000e+00 1.3483997249264841e+00
|
||||||
|
-6.7419986246324204e-01 6.7419986246324204e-01
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
|
2 1 0.6742 0.6742 0
|
||||||
11
examples/triclinic/dump.8Apr24.sq2.orthog.g++.4
Normal file
11
examples/triclinic/dump.8Apr24.sq2.orthog.g++.4
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
2
|
||||||
|
ITEM: BOX BOUNDS pp pp pp
|
||||||
|
0.0000000000000000e+00 1.3483997249264841e+00
|
||||||
|
0.0000000000000000e+00 1.3483997249264841e+00
|
||||||
|
-6.7419986246324204e-01 6.7419986246324204e-01
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
|
2 1 0.6742 0.6742 0
|
||||||
10
examples/triclinic/dump.8Apr24.sq2.primitive.g++.1
Normal file
10
examples/triclinic/dump.8Apr24.sq2.primitive.g++.1
Normal file
@ -0,0 +1,10 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
1
|
||||||
|
ITEM: BOX BOUNDS abc origin pp pp pp
|
||||||
|
6.7419986246324193e-01 -6.7419986246324204e-01 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
6.7419986246324193e-01 6.7419986246324204e-01 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
0.0000000000000000e+00 0.0000000000000000e+00 1.3483997249264841e+00 -6.7419986246324204e-01
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
10
examples/triclinic/dump.8Apr24.sq2.primitive.g++.4
Normal file
10
examples/triclinic/dump.8Apr24.sq2.primitive.g++.4
Normal file
@ -0,0 +1,10 @@
|
|||||||
|
ITEM: TIMESTEP
|
||||||
|
0
|
||||||
|
ITEM: NUMBER OF ATOMS
|
||||||
|
1
|
||||||
|
ITEM: BOX BOUNDS abc origin pp pp pp
|
||||||
|
6.7419986246324193e-01 -6.7419986246324204e-01 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
6.7419986246324193e-01 6.7419986246324204e-01 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
|
0.0000000000000000e+00 0.0000000000000000e+00 1.3483997249264841e+00 -6.7419986246324204e-01
|
||||||
|
ITEM: ATOMS id type x y z
|
||||||
|
1 1 0 0 0
|
||||||
23
examples/triclinic/in.bcc.orthog
Normal file
23
examples/triclinic/in.bcc.orthog
Normal file
@ -0,0 +1,23 @@
|
|||||||
|
# orthogonal box for bcc lattice unit cell
|
||||||
|
|
||||||
|
lattice bcc 1.0
|
||||||
|
|
||||||
|
region mybox block 0 1 0 1 0 1
|
||||||
|
create_box 1 mybox
|
||||||
|
create_atoms 1 box
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.bcc.orthog
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz &
|
||||||
|
cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.bcc.orthog id type x y z
|
||||||
|
|
||||||
|
run 0
|
||||||
25
examples/triclinic/in.bcc.primitive
Normal file
25
examples/triclinic/in.bcc.primitive
Normal file
@ -0,0 +1,25 @@
|
|||||||
|
# general triclinic box for bcc lattice primitive cell
|
||||||
|
|
||||||
|
lattice custom 1.0 a1 -0.5 0.5 0.5 a2 0.5 -0.5 0.5 a3 0.5 0.5 -0.5 &
|
||||||
|
basis 0.0 0.0 0.0 triclinic/general
|
||||||
|
|
||||||
|
create_box 1 NULL 0 1 0 1 0 1
|
||||||
|
create_atoms 1 box
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.bcc.primitive triclinic/general
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz &
|
||||||
|
cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.bcc.primitive id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
run 0
|
||||||
21
examples/triclinic/in.data.general
Normal file
21
examples/triclinic/in.data.general
Normal file
@ -0,0 +1,21 @@
|
|||||||
|
# read a general triclinic data file
|
||||||
|
|
||||||
|
read_data data.general
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.general triclinic/general
|
||||||
|
|
||||||
|
pair_style lj/cut 1.2
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz &
|
||||||
|
cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.general id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
run 0
|
||||||
23
examples/triclinic/in.fcc.orthog
Normal file
23
examples/triclinic/in.fcc.orthog
Normal file
@ -0,0 +1,23 @@
|
|||||||
|
# orthogonal box for fcc lattice unit cell
|
||||||
|
|
||||||
|
lattice fcc 1.1
|
||||||
|
|
||||||
|
region mybox block 0 1 0 1 0 1
|
||||||
|
create_box 1 mybox
|
||||||
|
create_atoms 1 box
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.fcc.orthog
|
||||||
|
|
||||||
|
pair_style lj/cut 1.2
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz &
|
||||||
|
cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.fcc.orthog id type x y z
|
||||||
|
|
||||||
|
run 0
|
||||||
25
examples/triclinic/in.fcc.primitive
Normal file
25
examples/triclinic/in.fcc.primitive
Normal file
@ -0,0 +1,25 @@
|
|||||||
|
# general triclinic box for fcc lattice primitive cell
|
||||||
|
|
||||||
|
lattice custom 1.1 a2 0.0 0.5 0.5 a3 0.5 0.0 0.5 a1 0.5 0.5 0.0 &
|
||||||
|
basis 0.0 0.0 0.0 triclinic/general
|
||||||
|
|
||||||
|
create_box 1 NULL 0 1 0 1 0 1
|
||||||
|
create_atoms 1 box
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.fcc.primitive triclinic/general
|
||||||
|
|
||||||
|
pair_style lj/cut 1.2
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz &
|
||||||
|
cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.fcc.primitive id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
run 0
|
||||||
24
examples/triclinic/in.hex.orthog
Normal file
24
examples/triclinic/in.hex.orthog
Normal file
@ -0,0 +1,24 @@
|
|||||||
|
# orthogonal box for 2d hex lattice unit cell
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice hex 1.0
|
||||||
|
|
||||||
|
region mybox block 0 1 0 1 -0.5 0.5
|
||||||
|
create_box 1 mybox
|
||||||
|
create_atoms 1 box
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.hex.orthog
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.hex.orthog id type x y z
|
||||||
|
|
||||||
|
run 0
|
||||||
26
examples/triclinic/in.hex.primitive
Normal file
26
examples/triclinic/in.hex.primitive
Normal file
@ -0,0 +1,26 @@
|
|||||||
|
# general triclinic box for 2d hex lattice primitive cell
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 &
|
||||||
|
a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general
|
||||||
|
|
||||||
|
create_box 1 NULL 0 1 0 1 -0.5 0.5
|
||||||
|
create_atoms 1 box
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.hex.primitive triclinic/general
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.hex.primitive id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
run 0
|
||||||
24
examples/triclinic/in.sq2.orthog
Normal file
24
examples/triclinic/in.sq2.orthog
Normal file
@ -0,0 +1,24 @@
|
|||||||
|
# orthogonal box for 2d sq2 lattice unit cell
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice sq2 1.1
|
||||||
|
|
||||||
|
region mybox block 0 1 0 1 -0.5 0.5
|
||||||
|
create_box 1 mybox
|
||||||
|
create_atoms 1 box
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.sq2.orthog
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.sq2.orthog id type x y z
|
||||||
|
|
||||||
|
run 0
|
||||||
26
examples/triclinic/in.sq2.primitive
Normal file
26
examples/triclinic/in.sq2.primitive
Normal file
@ -0,0 +1,26 @@
|
|||||||
|
# general triclinic box for 2d sq2 lattice primitive cell
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice custom 1.1 a1 0.5 -0.5 0.0 a2 0.5 0.5 0.0 a3 0.0 0.0 1.0 &
|
||||||
|
basis 0.0 0.0 0.0 triclinic/general
|
||||||
|
|
||||||
|
create_box 1 NULL 0 1 0 1 -0.5 0.5
|
||||||
|
create_atoms 1 box
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.sq2.primitive triclinic/general
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.sq2.primitive id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
run 0
|
||||||
74
examples/triclinic/log.8Apr24.bcc.orthog.g++.1
Normal file
74
examples/triclinic/log.8Apr24.bcc.orthog.g++.1
Normal file
@ -0,0 +1,74 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
# orthogonal box for bcc lattice unit cell
|
||||||
|
|
||||||
|
lattice bcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.259921 1.259921 1.259921
|
||||||
|
|
||||||
|
region mybox block 0 1 0 1 0 1
|
||||||
|
create_box 1 mybox
|
||||||
|
Created orthogonal box = (0 0 0) to (1.259921 1.259921 1.259921)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 2 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (1.259921 1.259921 1.259921)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.bcc.orthog
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.bcc.orthog id type x y z
|
||||||
|
|
||||||
|
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 = 1.1
|
||||||
|
ghost atom cutoff = 1.1
|
||||||
|
binsize = 0.55, bins = 3 3 3
|
||||||
|
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) = 3.058 | 3.058 | 3.058 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume
|
||||||
|
0 -3.8628258 1.259921 0 0 0 1.259921 0 0 0 1.259921 3.5116598 3.5116598 3.5116598 2
|
||||||
|
Loop time of 8.27e-07 on 1 procs for 0 steps with 2 atoms
|
||||||
|
|
||||||
|
120.9% CPU use with 1 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 | | 8.27e-07 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 2 ave 2 max 2 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 33 ave 33 max 33 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 8 ave 8 max 8 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 8
|
||||||
|
Ave neighs/atom = 4
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
75
examples/triclinic/log.8Apr24.bcc.orthog.g++.4
Normal file
75
examples/triclinic/log.8Apr24.bcc.orthog.g++.4
Normal file
@ -0,0 +1,75 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
|
||||||
|
# orthogonal box for bcc lattice unit cell
|
||||||
|
|
||||||
|
lattice bcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.259921 1.259921 1.259921
|
||||||
|
|
||||||
|
region mybox block 0 1 0 1 0 1
|
||||||
|
create_box 1 mybox
|
||||||
|
Created orthogonal box = (0 0 0) to (1.259921 1.259921 1.259921)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 2 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (1.259921 1.259921 1.259921)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.bcc.orthog
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.bcc.orthog id type x y z
|
||||||
|
|
||||||
|
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 = 1.1
|
||||||
|
ghost atom cutoff = 1.1
|
||||||
|
binsize = 0.55, bins = 3 3 3
|
||||||
|
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) = 2.948 | 3.011 | 3.073 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume
|
||||||
|
0 -3.8628258 1.259921 0 0 0 1.259921 0 0 0 1.259921 3.5116598 3.5116598 3.5116598 2
|
||||||
|
Loop time of 1.3815e-06 on 4 procs for 0 steps with 2 atoms
|
||||||
|
|
||||||
|
54.3% CPU use with 4 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 | | 1.382e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 0.5 ave 1 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 19.5 ave 20 max 19 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Neighs: 2 ave 4 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 8
|
||||||
|
Ave neighs/atom = 4
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
76
examples/triclinic/log.8Apr24.bcc.primitive.g++.1
Normal file
76
examples/triclinic/log.8Apr24.bcc.primitive.g++.1
Normal file
@ -0,0 +1,76 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
# general triclinic box for bcc lattice primitive cell
|
||||||
|
|
||||||
|
lattice custom 1.0 a1 -0.5 0.5 0.5 a2 0.5 -0.5 0.5 a3 0.5 0.5 -0.5 basis 0.0 0.0 0.0 triclinic/general
|
||||||
|
Lattice spacing in x,y,z = 1.8185394 1.5430818 0.89089872
|
||||||
|
|
||||||
|
create_box 1 NULL 0 1 0 1 0 1
|
||||||
|
Created triclinic box = (0 0 0) to (1.0911236 1.0287212 0.89089872) with tilt (-0.36370788 -0.36370788 -0.51436061)
|
||||||
|
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 1 atoms
|
||||||
|
using lattice units in triclinic box = (0 0 0) to (1.0911236 1.0287212 0.89089872) with tilt (-0.36370788 -0.36370788 -0.51436061)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.bcc.primitive triclinic/general
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.bcc.primitive id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
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 = 1.1
|
||||||
|
ghost atom cutoff = 1.1
|
||||||
|
binsize = 0.55, bins = 4 3 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton/tri
|
||||||
|
stencil: half/bin/3d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.084 | 3.084 | 3.084 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume
|
||||||
|
0 -3.8628258 -0.62996052 0.62996052 0.62996052 0.62996052 -0.62996052 0.62996052 0.62996052 0.62996052 -0.62996052 3.5116598 3.5116598 3.5116598 1
|
||||||
|
Loop time of 6.86e-07 on 1 procs for 0 steps with 1 atoms
|
||||||
|
|
||||||
|
145.8% CPU use with 1 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 | | 6.86e-07 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 1 ave 1 max 1 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 63 ave 63 max 63 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 4 ave 4 max 4 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 4
|
||||||
|
Ave neighs/atom = 4
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
77
examples/triclinic/log.8Apr24.bcc.primitive.g++.4
Normal file
77
examples/triclinic/log.8Apr24.bcc.primitive.g++.4
Normal file
@ -0,0 +1,77 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
|
||||||
|
# general triclinic box for bcc lattice primitive cell
|
||||||
|
|
||||||
|
lattice custom 1.0 a1 -0.5 0.5 0.5 a2 0.5 -0.5 0.5 a3 0.5 0.5 -0.5 basis 0.0 0.0 0.0 triclinic/general
|
||||||
|
Lattice spacing in x,y,z = 1.8185394 1.5430818 0.89089872
|
||||||
|
|
||||||
|
create_box 1 NULL 0 1 0 1 0 1
|
||||||
|
Created triclinic box = (0 0 0) to (1.0911236 1.0287212 0.89089872) with tilt (-0.36370788 -0.36370788 -0.51436061)
|
||||||
|
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 1 atoms
|
||||||
|
using lattice units in triclinic box = (0 0 0) to (1.0911236 1.0287212 0.89089872) with tilt (-0.36370788 -0.36370788 -0.51436061)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.bcc.primitive triclinic/general
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.bcc.primitive id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
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 = 1.1
|
||||||
|
ghost atom cutoff = 1.1
|
||||||
|
binsize = 0.55, bins = 4 3 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton/tri
|
||||||
|
stencil: half/bin/3d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.973 | 3.005 | 3.098 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume
|
||||||
|
0 -3.8628258 -0.62996052 0.62996052 0.62996052 0.62996052 -0.62996052 0.62996052 0.62996052 0.62996052 -0.62996052 3.5116598 3.5116598 3.5116598 1
|
||||||
|
Loop time of 2.1275e-06 on 4 procs for 0 steps with 1 atoms
|
||||||
|
|
||||||
|
70.5% CPU use with 4 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 | | 2.127e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 0.25 ave 1 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 35.75 ave 36 max 35 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 1 ave 4 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 4
|
||||||
|
Ave neighs/atom = 4
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
73
examples/triclinic/log.8Apr24.data.general.g++.1
Normal file
73
examples/triclinic/log.8Apr24.data.general.g++.1
Normal file
@ -0,0 +1,73 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
# read a general triclinic data file
|
||||||
|
|
||||||
|
read_data data.general
|
||||||
|
Reading data file ...
|
||||||
|
triclinic box = (0 0 0) to (1.4142136 1.4142136 1) with tilt (-1.110223e-16 -1.110223e-16 1.4142136)
|
||||||
|
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2 atoms
|
||||||
|
read_data CPU = 0.001 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.general triclinic/general
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.2
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.general id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
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 = 1.2
|
||||||
|
ghost atom cutoff = 1.2
|
||||||
|
binsize = 0.6, bins = 3 5 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton/tri
|
||||||
|
stencil: half/bin/3d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.076 | 3.076 | 3.076 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume
|
||||||
|
0 456.05603 1 -1 0 1 1 0 1 1 1 2555.5604 2555.5604 598.94037 2
|
||||||
|
Loop time of 7.31e-07 on 1 procs for 0 steps with 2 atoms
|
||||||
|
|
||||||
|
136.8% CPU use with 1 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 | | 7.31e-07 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 2 ave 2 max 2 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 66 ave 66 max 66 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 6 ave 6 max 6 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 6
|
||||||
|
Ave neighs/atom = 3
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
74
examples/triclinic/log.8Apr24.data.general.g++.4
Normal file
74
examples/triclinic/log.8Apr24.data.general.g++.4
Normal file
@ -0,0 +1,74 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
|
||||||
|
# read a general triclinic data file
|
||||||
|
|
||||||
|
read_data data.general
|
||||||
|
Reading data file ...
|
||||||
|
triclinic box = (0 0 0) to (1.4142136 1.4142136 1) with tilt (-1.110223e-16 -1.110223e-16 1.4142136)
|
||||||
|
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2 atoms
|
||||||
|
read_data CPU = 0.001 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.general triclinic/general
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.2
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.general id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
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 = 1.2
|
||||||
|
ghost atom cutoff = 1.2
|
||||||
|
binsize = 0.6, bins = 3 5 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton/tri
|
||||||
|
stencil: half/bin/3d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.966 | 2.997 | 3.091 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume
|
||||||
|
0 456.05603 1 -1 0 1 1 0 1 1 1 2555.5604 2555.5604 598.94037 2
|
||||||
|
Loop time of 2.13e-06 on 4 procs for 0 steps with 2 atoms
|
||||||
|
|
||||||
|
70.4% CPU use with 4 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 | | 2.13e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 0.5 ave 2 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 47.5 ave 48 max 46 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 1.5 ave 6 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 6
|
||||||
|
Ave neighs/atom = 3
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
74
examples/triclinic/log.8Apr24.fcc.orthog.g++.1
Normal file
74
examples/triclinic/log.8Apr24.fcc.orthog.g++.1
Normal file
@ -0,0 +1,74 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
# orthogonal box for fcc lattice unit cell
|
||||||
|
|
||||||
|
lattice fcc 1.1
|
||||||
|
Lattice spacing in x,y,z = 1.5377619 1.5377619 1.5377619
|
||||||
|
|
||||||
|
region mybox block 0 1 0 1 0 1
|
||||||
|
create_box 1 mybox
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5377619 1.5377619 1.5377619)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 4 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (1.5377619 1.5377619 1.5377619)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.fcc.orthog
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.2
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.fcc.orthog id type x y z
|
||||||
|
|
||||||
|
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 = 1.2
|
||||||
|
ghost atom cutoff = 1.2
|
||||||
|
binsize = 0.6, bins = 3 3 3
|
||||||
|
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) = 3.059 | 3.059 | 3.059 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume
|
||||||
|
0 -5.7354 1.5377619 0 0 0 1.5377619 0 0 0 1.5377619 6.70824 6.70824 6.70824 3.6363636
|
||||||
|
Loop time of 8.53e-07 on 1 procs for 0 steps with 4 atoms
|
||||||
|
|
||||||
|
0.0% CPU use with 1 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 | | 8.53e-07 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 4 ave 4 max 4 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 58 ave 58 max 58 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 24 ave 24 max 24 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 24
|
||||||
|
Ave neighs/atom = 6
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
75
examples/triclinic/log.8Apr24.fcc.orthog.g++.4
Normal file
75
examples/triclinic/log.8Apr24.fcc.orthog.g++.4
Normal file
@ -0,0 +1,75 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
|
||||||
|
# orthogonal box for fcc lattice unit cell
|
||||||
|
|
||||||
|
lattice fcc 1.1
|
||||||
|
Lattice spacing in x,y,z = 1.5377619 1.5377619 1.5377619
|
||||||
|
|
||||||
|
region mybox block 0 1 0 1 0 1
|
||||||
|
create_box 1 mybox
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5377619 1.5377619 1.5377619)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 4 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (1.5377619 1.5377619 1.5377619)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.fcc.orthog
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.2
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.fcc.orthog id type x y z
|
||||||
|
|
||||||
|
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 = 1.2
|
||||||
|
ghost atom cutoff = 1.2
|
||||||
|
binsize = 0.6, bins = 3 3 3
|
||||||
|
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) = 3.074 | 3.074 | 3.074 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume
|
||||||
|
0 -5.7354 1.5377619 0 0 0 1.5377619 0 0 0 1.5377619 6.70824 6.70824 6.70824 3.6363636
|
||||||
|
Loop time of 3.291e-06 on 4 procs for 0 steps with 4 atoms
|
||||||
|
|
||||||
|
76.0% CPU use with 4 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 | | 3.291e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 1 ave 1 max 1 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 39 ave 39 max 39 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 6 ave 6 max 6 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 24
|
||||||
|
Ave neighs/atom = 6
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
76
examples/triclinic/log.8Apr24.fcc.primitive.g++.1
Normal file
76
examples/triclinic/log.8Apr24.fcc.primitive.g++.1
Normal file
@ -0,0 +1,76 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
# general triclinic box for fcc lattice primitive cell
|
||||||
|
|
||||||
|
lattice custom 1.1 a2 0.0 0.5 0.5 a3 0.5 0.0 0.5 a1 0.5 0.5 0.0 basis 0.0 0.0 0.0 triclinic/general
|
||||||
|
Lattice spacing in x,y,z = 2.1747238 1.2555773 0.88782726
|
||||||
|
|
||||||
|
create_box 1 NULL 0 1 0 1 0 1
|
||||||
|
Created triclinic box = (0 0 0) to (1.0873619 0.94168301 0.88782726) with tilt (0.54368094 0.54368094 0.31389434)
|
||||||
|
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 1 atoms
|
||||||
|
using lattice units in triclinic box = (0 0 0) to (1.0873619 0.94168301 0.88782726) with tilt (0.54368094 0.54368094 0.31389434)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.fcc.primitive triclinic/general
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.2
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.fcc.primitive id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
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 = 1.2
|
||||||
|
ghost atom cutoff = 1.2
|
||||||
|
binsize = 0.6, bins = 4 3 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton/tri
|
||||||
|
stencil: half/bin/3d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.084 | 3.084 | 3.084 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume
|
||||||
|
0 -5.7354 0.76888096 0.76888096 -6.036071e-17 -5.5511151e-17 0.76888096 0.76888096 0.76888096 0 0.76888096 6.70824 6.70824 6.70824 0.90909091
|
||||||
|
Loop time of 8.83e-07 on 1 procs for 0 steps with 1 atoms
|
||||||
|
|
||||||
|
0.0% CPU use with 1 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 | | 8.83e-07 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 1 ave 1 max 1 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 63 ave 63 max 63 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 6 ave 6 max 6 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 6
|
||||||
|
Ave neighs/atom = 6
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
77
examples/triclinic/log.8Apr24.fcc.primitive.g++.4
Normal file
77
examples/triclinic/log.8Apr24.fcc.primitive.g++.4
Normal file
@ -0,0 +1,77 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
|
||||||
|
# general triclinic box for fcc lattice primitive cell
|
||||||
|
|
||||||
|
lattice custom 1.1 a2 0.0 0.5 0.5 a3 0.5 0.0 0.5 a1 0.5 0.5 0.0 basis 0.0 0.0 0.0 triclinic/general
|
||||||
|
Lattice spacing in x,y,z = 2.1747238 1.2555773 0.88782726
|
||||||
|
|
||||||
|
create_box 1 NULL 0 1 0 1 0 1
|
||||||
|
Created triclinic box = (0 0 0) to (1.0873619 0.94168301 0.88782726) with tilt (0.54368094 0.54368094 0.31389434)
|
||||||
|
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 1 atoms
|
||||||
|
using lattice units in triclinic box = (0 0 0) to (1.0873619 0.94168301 0.88782726) with tilt (0.54368094 0.54368094 0.31389434)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.fcc.primitive triclinic/general
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.2
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy avecz bvecx bvecy bvecz cvecx cvecy cvecz pxx pyy pzz vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.fcc.primitive id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
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 = 1.2
|
||||||
|
ghost atom cutoff = 1.2
|
||||||
|
binsize = 0.6, bins = 4 3 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton/tri
|
||||||
|
stencil: half/bin/3d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.973 | 3.005 | 3.098 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Avecz Bvecx Bvecy Bvecz Cvecx Cvecy Cvecz Pxx Pyy Pzz Volume
|
||||||
|
0 -5.7354 0.76888096 0.76888096 -6.036071e-17 -5.5511151e-17 0.76888096 0.76888096 0.76888096 0 0.76888096 6.70824 6.70824 6.70824 0.90909091
|
||||||
|
Loop time of 1.7905e-06 on 4 procs for 0 steps with 1 atoms
|
||||||
|
|
||||||
|
55.9% CPU use with 4 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 | | 1.791e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 0.25 ave 1 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 35.75 ave 36 max 35 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 1.5 ave 6 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 6
|
||||||
|
Ave neighs/atom = 6
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
76
examples/triclinic/log.8Apr24.hex.orthog.g++.1
Normal file
76
examples/triclinic/log.8Apr24.hex.orthog.g++.1
Normal file
@ -0,0 +1,76 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
# orthogonal box for 2d hex lattice unit cell
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice hex 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
|
||||||
|
|
||||||
|
region mybox block 0 1 0 1 -0.5 0.5
|
||||||
|
create_box 1 mybox
|
||||||
|
Created orthogonal box = (0 0 -0.53728497) to (1.0745699 1.8612097 0.53728497)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 2 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 -0.53728497) to (1.0745699 1.8612097 0.53728497)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.hex.orthog
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.hex.orthog id type x y z
|
||||||
|
|
||||||
|
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 = 1.1
|
||||||
|
ghost atom cutoff = 1.1
|
||||||
|
binsize = 0.55, bins = 2 4 2
|
||||||
|
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/2d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.054 | 3.054 | 3.054 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume
|
||||||
|
0 -2.7317286 1.0745699 0 0 1.8612097 6.9923141 6.9923141 2
|
||||||
|
Loop time of 9.26e-07 on 1 procs for 0 steps with 2 atoms
|
||||||
|
|
||||||
|
0.0% CPU use with 1 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 | | 9.26e-07 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 2 ave 2 max 2 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 15 ave 15 max 15 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 6 ave 6 max 6 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 6
|
||||||
|
Ave neighs/atom = 3
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
77
examples/triclinic/log.8Apr24.hex.orthog.g++.4
Normal file
77
examples/triclinic/log.8Apr24.hex.orthog.g++.4
Normal file
@ -0,0 +1,77 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
|
||||||
|
# orthogonal box for 2d hex lattice unit cell
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice hex 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
|
||||||
|
|
||||||
|
region mybox block 0 1 0 1 -0.5 0.5
|
||||||
|
create_box 1 mybox
|
||||||
|
Created orthogonal box = (0 0 -0.53728497) to (1.0745699 1.8612097 0.53728497)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 2 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 -0.53728497) to (1.0745699 1.8612097 0.53728497)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.hex.orthog
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.hex.orthog id type x y z
|
||||||
|
|
||||||
|
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 = 1.1
|
||||||
|
ghost atom cutoff = 1.1
|
||||||
|
binsize = 0.55, bins = 2 4 2
|
||||||
|
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/2d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.945 | 2.945 | 2.945 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume
|
||||||
|
0 -2.7317286 1.0745699 0 0 1.8612097 6.9923141 6.9923141 2
|
||||||
|
Loop time of 1.9155e-06 on 4 procs for 0 steps with 2 atoms
|
||||||
|
|
||||||
|
52.2% CPU use with 4 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 | | 1.915e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 0.5 ave 1 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 11.5 ave 12 max 11 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Neighs: 1.5 ave 3 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 6
|
||||||
|
Ave neighs/atom = 3
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
78
examples/triclinic/log.8Apr24.hex.primitive.g++.1
Normal file
78
examples/triclinic/log.8Apr24.hex.primitive.g++.1
Normal file
@ -0,0 +1,78 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
# general triclinic box for 2d hex lattice primitive cell
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general
|
||||||
|
Lattice spacing in x,y,z = 1.6118549 0.93060486 1.0745699
|
||||||
|
|
||||||
|
create_box 1 NULL 0 1 0 1 -0.5 0.5
|
||||||
|
Created triclinic box = (0 0 -0.53728497) to (1.0745699 0.93060486 0.53728497) with tilt (0.53728497 0 0)
|
||||||
|
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 1 atoms
|
||||||
|
using lattice units in triclinic box = (0 0 -0.53728497) to (1.0745699 0.93060486 0.53728497) with tilt (0.53728497 0 0)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.hex.primitive triclinic/general
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.hex.primitive id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
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 = 1.1
|
||||||
|
ghost atom cutoff = 1.1
|
||||||
|
binsize = 0.55, bins = 3 2 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton/tri
|
||||||
|
stencil: half/bin/2d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume
|
||||||
|
0 -2.7317286 1.0745699 0 0.53728497 0.93060486 6.9923141 6.9923141 1
|
||||||
|
Loop time of 1.03e-06 on 1 procs for 0 steps with 1 atoms
|
||||||
|
|
||||||
|
97.1% CPU use with 1 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 | | 1.03e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 1 ave 1 max 1 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 15 ave 15 max 15 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 3 ave 3 max 3 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 3
|
||||||
|
Ave neighs/atom = 3
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
79
examples/triclinic/log.8Apr24.hex.primitive.g++.4
Normal file
79
examples/triclinic/log.8Apr24.hex.primitive.g++.4
Normal file
@ -0,0 +1,79 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
|
||||||
|
# general triclinic box for 2d hex lattice primitive cell
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general
|
||||||
|
Lattice spacing in x,y,z = 1.6118549 0.93060486 1.0745699
|
||||||
|
|
||||||
|
create_box 1 NULL 0 1 0 1 -0.5 0.5
|
||||||
|
Created triclinic box = (0 0 -0.53728497) to (1.0745699 0.93060486 0.53728497) with tilt (0.53728497 0 0)
|
||||||
|
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (../domain.cpp:221)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 1 atoms
|
||||||
|
using lattice units in triclinic box = (0 0 -0.53728497) to (1.0745699 0.93060486 0.53728497) with tilt (0.53728497 0 0)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.hex.primitive triclinic/general
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.hex.primitive id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
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 = 1.1
|
||||||
|
ghost atom cutoff = 1.1
|
||||||
|
binsize = 0.55, bins = 3 2 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton/tri
|
||||||
|
stencil: half/bin/2d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.953 | 2.953 | 2.953 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume
|
||||||
|
0 -2.7317286 1.0745699 0 0.53728497 0.93060486 6.9923141 6.9923141 1
|
||||||
|
Loop time of 2.45225e-06 on 4 procs for 0 steps with 1 atoms
|
||||||
|
|
||||||
|
61.2% CPU use with 4 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 | | 2.452e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 0.25 ave 1 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 8.75 ave 9 max 8 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 0.75 ave 3 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 3
|
||||||
|
Ave neighs/atom = 3
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
76
examples/triclinic/log.8Apr24.sq2.orthog.g++.1
Normal file
76
examples/triclinic/log.8Apr24.sq2.orthog.g++.1
Normal file
@ -0,0 +1,76 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
# orthogonal box for 2d sq2 lattice unit cell
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice sq2 1.1
|
||||||
|
Lattice spacing in x,y,z = 1.3483997 1.3483997 1.3483997
|
||||||
|
|
||||||
|
region mybox block 0 1 0 1 -0.5 0.5
|
||||||
|
create_box 1 mybox
|
||||||
|
Created orthogonal box = (0 0 -0.67419986) to (1.3483997 1.3483997 0.67419986)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 2 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 -0.67419986) to (1.3483997 1.3483997 0.67419986)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.sq2.orthog
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.sq2.orthog id type x y z
|
||||||
|
|
||||||
|
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 = 1.1
|
||||||
|
ghost atom cutoff = 1.1
|
||||||
|
binsize = 0.55, bins = 3 3 3
|
||||||
|
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/2d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.046 | 3.046 | 3.046 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume
|
||||||
|
0 3.524488 1.3483997 0 0 1.3483997 58.400021 58.400021 1.8181818
|
||||||
|
Loop time of 9.37e-07 on 1 procs for 0 steps with 2 atoms
|
||||||
|
|
||||||
|
106.7% CPU use with 1 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 | | 9.37e-07 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 2 ave 2 max 2 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 11 ave 11 max 11 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 4 ave 4 max 4 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 4
|
||||||
|
Ave neighs/atom = 2
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
77
examples/triclinic/log.8Apr24.sq2.orthog.g++.4
Normal file
77
examples/triclinic/log.8Apr24.sq2.orthog.g++.4
Normal file
@ -0,0 +1,77 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
|
||||||
|
# orthogonal box for 2d sq2 lattice unit cell
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice sq2 1.1
|
||||||
|
Lattice spacing in x,y,z = 1.3483997 1.3483997 1.3483997
|
||||||
|
|
||||||
|
region mybox block 0 1 0 1 -0.5 0.5
|
||||||
|
create_box 1 mybox
|
||||||
|
Created orthogonal box = (0 0 -0.67419986) to (1.3483997 1.3483997 0.67419986)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 2 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 -0.67419986) to (1.3483997 1.3483997 0.67419986)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.sq2.orthog
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.sq2.orthog id type x y z
|
||||||
|
|
||||||
|
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 = 1.1
|
||||||
|
ghost atom cutoff = 1.1
|
||||||
|
binsize = 0.55, bins = 3 3 3
|
||||||
|
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/2d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.937 | 2.937 | 2.937 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume
|
||||||
|
0 3.524488 1.3483997 0 0 1.3483997 58.400021 58.400021 1.8181818
|
||||||
|
Loop time of 1.703e-06 on 4 procs for 0 steps with 2 atoms
|
||||||
|
|
||||||
|
29.4% CPU use with 4 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 | | 1.703e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 0.5 ave 1 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 7.5 ave 8 max 7 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Neighs: 1 ave 2 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 4
|
||||||
|
Ave neighs/atom = 2
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
77
examples/triclinic/log.8Apr24.sq2.primitive.g++.1
Normal file
77
examples/triclinic/log.8Apr24.sq2.primitive.g++.1
Normal file
@ -0,0 +1,77 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
# general triclinic box for 2d sq2 lattice primitive cell
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice custom 1.1 a1 0.5 -0.5 0.0 a2 0.5 0.5 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general
|
||||||
|
Lattice spacing in x,y,z = 0.95346259 0.95346259 1.3483997
|
||||||
|
|
||||||
|
create_box 1 NULL 0 1 0 1 -0.5 0.5
|
||||||
|
Created triclinic box = (0 0 -0.67419986) to (0.95346259 0.95346259 0.67419986) with tilt (-1.110223e-16 0 0)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 1 atoms
|
||||||
|
using lattice units in triclinic box = (0 0 -0.67419986) to (0.95346259 0.95346259 0.67419986) with tilt (-1.110223e-16 0 0)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.sq2.primitive triclinic/general
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.sq2.primitive id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
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 = 1.1
|
||||||
|
ghost atom cutoff = 1.1
|
||||||
|
binsize = 0.55, bins = 2 2 3
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton/tri
|
||||||
|
stencil: half/bin/2d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.937 | 2.937 | 2.937 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume
|
||||||
|
0 3.524488 0.67419986 -0.67419986 0.67419986 0.67419986 58.400021 58.400021 0.90909091
|
||||||
|
Loop time of 8.38e-07 on 1 procs for 0 steps with 1 atoms
|
||||||
|
|
||||||
|
119.3% CPU use with 1 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 | | 8.38e-07 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 1 ave 1 max 1 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 15 ave 15 max 15 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 2 ave 2 max 2 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 2
|
||||||
|
Ave neighs/atom = 2
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
78
examples/triclinic/log.8Apr24.sq2.primitive.g++.4
Normal file
78
examples/triclinic/log.8Apr24.sq2.primitive.g++.4
Normal file
@ -0,0 +1,78 @@
|
|||||||
|
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-442-gf1c2a22e2d)
|
||||||
|
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
|
||||||
|
# general triclinic box for 2d sq2 lattice primitive cell
|
||||||
|
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice custom 1.1 a1 0.5 -0.5 0.0 a2 0.5 0.5 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general
|
||||||
|
Lattice spacing in x,y,z = 0.95346259 0.95346259 1.3483997
|
||||||
|
|
||||||
|
create_box 1 NULL 0 1 0 1 -0.5 0.5
|
||||||
|
Created triclinic box = (0 0 -0.67419986) to (0.95346259 0.95346259 0.67419986) with tilt (-1.110223e-16 0 0)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 1 atoms
|
||||||
|
using lattice units in triclinic box = (0 0 -0.67419986) to (0.95346259 0.95346259 0.67419986) with tilt (-1.110223e-16 0 0)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
write_data tmp.data.sq2.primitive triclinic/general
|
||||||
|
System init for write_data ...
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
|
||||||
|
pair_style lj/cut 1.1
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step pe avecx avecy bvecx bvecy pxx pyy vol
|
||||||
|
thermo_modify triclinic/general yes
|
||||||
|
|
||||||
|
dump 1 all custom 100 tmp.dump.sq2.primitive id type x y z
|
||||||
|
dump_modify 1 triclinic/general yes
|
||||||
|
|
||||||
|
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 = 1.1
|
||||||
|
ghost atom cutoff = 1.1
|
||||||
|
binsize = 0.55, bins = 2 2 3
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton/tri
|
||||||
|
stencil: half/bin/2d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.953 | 2.953 | 2.953 Mbytes
|
||||||
|
Step PotEng Avecx Avecy Bvecx Bvecy Pxx Pyy Volume
|
||||||
|
0 3.524488 0.67419986 -0.67419986 0.67419986 0.67419986 58.400021 58.400021 0.90909091
|
||||||
|
Loop time of 1.91525e-06 on 4 procs for 0 steps with 1 atoms
|
||||||
|
|
||||||
|
52.2% CPU use with 4 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 | | 1.915e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 0.25 ave 1 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 8.75 ave 9 max 8 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 0.5 ave 2 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 2
|
||||||
|
Ave neighs/atom = 2
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
Reference in New Issue
Block a user