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correctly enable GPU package and make fix imd wait in background for bucky+cnt example

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This commit is contained in:
Axel Kohlmeyer
2025-05-15 08:15:01 -04:00
parent 179d4f0148
commit 19cfd08eb8
4 changed files with 38 additions and 33 deletions
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4
examples/PACKAGES/imd/in.bucky-plus-cnt
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@ -46,8 +46,8 @@ fix integrate mobile nve
fix thermostat mobile langevin 300.0 300.0 2000.0 234624 fix thermostat mobile langevin 300.0 300.0 2000.0 234624
# IMD setup. # IMD setup.
fix comm all imd 6789 unwrap on trate 10 #fix comm all imd 6789 unwrap on trate 10
#fix comm all imd 6789 unwrap on trate 10 nowait on fix comm all imd 6789 unwrap on trate 10 nowait on
# temperature is based on mobile atoms only # temperature is based on mobile atoms only
compute mobtemp mobile temp compute mobtemp mobile temp

15
examples/PACKAGES/imd/in.bucky-plus-cnt-gpu
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@ -1,16 +1,20 @@
# stick a buckyball into a nanotube # stick a buckyball into a nanotube
# enable GPU package from within the input:
package gpu 0 pair/only on
suffix gpu
units real units real
dimension 3 dimension 3
boundary f f f boundary f f f
atom_style molecular atom_style molecular
newton off
processors * * 1 processors * * 1
# read topology # read topology
read_data data.bucky-plus-cnt read_data data.bucky-plus-cnt
pair_style lj/cut/gpu 10.0 pair_style lj/cut 10.0
bond_style harmonic bond_style harmonic
angle_style charmm angle_style charmm
dihedral_style charmm dihedral_style charmm
@ -29,9 +33,6 @@ neigh_modify delay 0 every 1 check yes
timestep 2.0 timestep 2.0
# required for GPU acceleration
fix gpu all gpu force 0 0 1.0
# we only move some atoms. # we only move some atoms.
group mobile type 1 group mobile type 1
@ -49,8 +50,8 @@ fix integrate mobile nve
fix thermostat mobile langevin 300.0 300.0 2000.0 234624 fix thermostat mobile langevin 300.0 300.0 2000.0 234624
# IMD setup. # IMD setup.
fix comm all imd 6789 unwrap on trate 10 #fix comm all imd 6789 unwrap on trate 10
#fix comm all imd 6789 unwrap on trate 10 nowait on fix comm all imd 6789 unwrap on trate 10 nowait on
# temperature is based on mobile atoms only # temperature is based on mobile atoms only
compute mobtemp mobile temp compute mobtemp mobile temp

12
examples/PACKAGES/imd/in.deca-ala_imd-gpu
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@ -1,8 +1,12 @@
# #
# enable GPU package from within the input:
package gpu 0 pair/only on
suffix gpu
units real units real
neighbor 2.5 bin neighbor 2.5 bin
neigh_modify delay 1 every 1 neigh_modify delay 1 every 1
newton off
atom_style full atom_style full
bond_style harmonic bond_style harmonic
@ -10,20 +14,18 @@ angle_style charmm
dihedral_style charmm dihedral_style charmm
improper_style harmonic improper_style harmonic
pair_style lj/charmm/coul/long/gpu 8 10 pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic pair_modify mix arithmetic
special_bonds charmm special_bonds charmm
read_data data.deca-ala-solv read_data data.deca-ala-solv
fix 0 all gpu force/neigh 0 0 1.0
group peptide id <= 103 group peptide id <= 103
fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23 fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
thermo 100 thermo 100
thermo_style multi thermo_style multi
timestep 2.0 timestep 2.0
kspace_style pppm/gpu 1e-5 kspace_style pppm 1e-5
fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2 fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2

10
examples/PACKAGES/imd/in.melt_imd-gpu
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@ -1,8 +1,11 @@
# 3d Lennard-Jones melt # 3d Lennard-Jones melt with GPU package acceleration
# enable GPU package from within the input:
package gpu 0
suffix gpu
units lj units lj
atom_style atomic atom_style atomic
newton off
lattice fcc 0.8442 lattice fcc 0.8442
region box block 0 10 0 10 0 10 region box block 0 10 0 10 0 10
@ -12,7 +15,7 @@ mass 1 1.0
velocity all create 3.0 87287 velocity all create 3.0 87287
pair_style lj/cut/gpu 2.5 pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5 pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin neighbor 0.3 bin
@ -20,7 +23,6 @@ neigh_modify every 5 delay 10 check yes
thermo_style custom step pe ke spcpu thermo_style custom step pe ke spcpu
fix 0 all gpu force/neigh 0 0 1.0
fix 1 all nve fix 1 all nve
# IMD setup. # IMD setup.