forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12784 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
8c274c9af2
commit
223eea1510
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@ -0,0 +1,196 @@
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para-Hydrogen density=0.023500
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180 atoms
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1 atom types
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0.000000 19.712190 xlo xhi
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0.000000 19.712190 ylo yhi
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0.000000 19.712190 zlo zhi
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Masses
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1 0.5
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|
||||
D 11.827314 3.285365 3.285365
|
||||
D 11.827314 3.285365 6.570730
|
||||
D 11.827314 3.285365 9.856095
|
||||
D 11.827314 3.285365 13.141460
|
||||
D 11.827314 3.285365 16.426825
|
||||
D 11.827314 6.570730 0.000000
|
||||
D 11.827314 6.570730 3.285365
|
||||
D 11.827314 6.570730 6.570730
|
||||
D 11.827314 6.570730 9.856095
|
||||
D 11.827314 6.570730 13.141460
|
||||
D 11.827314 6.570730 16.426825
|
||||
D 11.827314 9.856095 0.000000
|
||||
D 11.827314 9.856095 3.285365
|
||||
D 11.827314 9.856095 6.570730
|
||||
D 11.827314 9.856095 9.856095
|
||||
D 11.827314 9.856095 13.141460
|
||||
D 11.827314 9.856095 16.426825
|
||||
D 11.827314 13.141460 0.000000
|
||||
D 11.827314 13.141460 3.285365
|
||||
D 11.827314 13.141460 6.570730
|
||||
D 11.827314 13.141460 9.856095
|
||||
D 11.827314 13.141460 13.141460
|
||||
D 11.827314 13.141460 16.426825
|
||||
D 11.827314 16.426825 0.000000
|
||||
D 11.827314 16.426825 3.285365
|
||||
D 11.827314 16.426825 6.570730
|
||||
D 11.827314 16.426825 9.856095
|
||||
D 11.827314 16.426825 13.141460
|
||||
D 11.827314 16.426825 16.426825
|
||||
D 15.769752 0.000000 0.000000
|
||||
D 15.769752 0.000000 3.285365
|
||||
D 15.769752 0.000000 6.570730
|
||||
D 15.769752 0.000000 9.856095
|
||||
D 15.769752 0.000000 13.141460
|
||||
D 15.769752 0.000000 16.426825
|
||||
D 15.769752 3.285365 0.000000
|
||||
D 15.769752 3.285365 3.285365
|
||||
D 15.769752 3.285365 6.570730
|
||||
D 15.769752 3.285365 9.856095
|
||||
D 15.769752 3.285365 13.141460
|
||||
D 15.769752 3.285365 16.426825
|
||||
D 15.769752 6.570730 0.000000
|
||||
D 15.769752 6.570730 3.285365
|
||||
D 15.769752 6.570730 6.570730
|
||||
D 15.769752 6.570730 9.856095
|
||||
D 15.769752 6.570730 13.141460
|
||||
D 15.769752 6.570730 16.426825
|
||||
D 15.769752 9.856095 0.000000
|
||||
D 15.769752 9.856095 3.285365
|
||||
D 15.769752 9.856095 6.570730
|
||||
D 15.769752 9.856095 9.856095
|
||||
D 15.769752 9.856095 13.141460
|
||||
D 15.769752 9.856095 16.426825
|
||||
D 15.769752 13.141460 0.000000
|
||||
D 15.769752 13.141460 3.285365
|
||||
D 15.769752 13.141460 6.570730
|
||||
D 15.769752 13.141460 9.856095
|
||||
D 15.769752 13.141460 13.141460
|
||||
D 15.769752 13.141460 16.426825
|
||||
D 15.769752 16.426825 0.000000
|
||||
D 15.769752 16.426825 3.285365
|
||||
D 15.769752 16.426825 6.570730
|
||||
D 15.769752 16.426825 9.856095
|
||||
D 15.769752 16.426825 13.141460
|
||||
D 15.769752 16.426825 16.426825
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
EIGENVALUES
|
||||
|
||||
1 0.00000000
|
||||
2 4.68629150
|
||||
3 4.68629150
|
||||
4 16.00000000
|
||||
5 16.00000000
|
||||
6 27.31370850
|
||||
7 27.31370850
|
||||
8 32.00000000
|
||||
|
||||
EIGENVECTORS
|
||||
|
||||
0.12500000 0.17677670 -0.00000000 0.17677670 -0.00000000 0.17677670 -0.00000000 0.12500000
|
||||
0.12500000 0.12500000 -0.12500000 0.00000000 -0.17677670 -0.12500000 -0.12500000 -0.12500000
|
||||
0.12500000 0.00000000 -0.17677670 -0.17677670 -0.00000000 -0.00000000 0.17677670 0.12500000
|
||||
0.12500000 -0.12500000 -0.12500000 -0.00000000 0.17677670 0.12500000 -0.12500000 -0.12500000
|
||||
0.12500000 -0.17677670 -0.00000000 0.17677670 0.00000000 -0.17677670 -0.00000000 0.12500000
|
||||
0.12500000 -0.12500000 0.12500000 0.00000000 -0.17677670 0.12500000 0.12500000 -0.12500000
|
||||
0.12500000 -0.00000000 0.17677670 -0.17677670 -0.00000000 0.00000000 -0.17677670 0.12500000
|
||||
0.12500000 0.12500000 0.12500000 -0.00000000 0.17677670 -0.12500000 0.12500000 -0.12500000
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
variable ibead uloop 32 pad
|
||||
variable out_freq string 1
|
||||
variable job_name string H2
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
pair_style table linear 10000
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check no
|
||||
|
||||
read_data H2.data
|
||||
|
||||
pair_coeff 1 * pair.table PAIR_H2
|
||||
|
||||
timestep 0.001
|
||||
|
||||
thermo_style custom step temp pe etotal pzz
|
||||
thermo ${out_freq}
|
||||
|
||||
velocity all create 1.0 1985 rot yes dist gaussian
|
||||
|
||||
fix 1 all quantum method nmpimd fmass 1.0 temp 25.0 nhc 4
|
||||
|
||||
dump dcd all dcd ${out_freq} dcd/${job_name}_${ibead}.dcd
|
||||
|
||||
restart ${out_freq} restart/${job_name}_${ibead}.restart1 restart/${job_name}_${ibead}.restart2
|
||||
|
||||
run 100000
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1 @@
|
|||
mpirun -np 64 lmp_mpi -partition 8x8 -in in.scp -log logfile/log.lammps -screen screen/screen
|
||||
|
|
@ -0,0 +1,94 @@
|
|||
###################################################################
|
||||
|
||||
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
animate delete beg 0 end 0 skip 0 0
|
||||
mol addfile dcd/H2_0.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
|
||||
mol representation CPK
|
||||
mol color Name
|
||||
mol material Opaque
|
||||
mol addrep top
|
||||
|
||||
|
||||
###################################################################
|
||||
|
||||
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
animate delete beg 0 end 0 skip 0 1
|
||||
mol addfile dcd/H2_1.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
|
||||
mol representation CPK
|
||||
mol color Name
|
||||
mol material Opaque
|
||||
mol addrep top
|
||||
|
||||
###################################################################
|
||||
|
||||
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
animate delete beg 0 end 0 skip 0 2
|
||||
mol addfile dcd/H2_2.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
|
||||
mol representation CPK
|
||||
mol color Name
|
||||
mol material Opaque
|
||||
mol addrep top
|
||||
|
||||
###################################################################
|
||||
|
||||
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
animate delete beg 0 end 0 skip 0 3
|
||||
mol addfile dcd/H2_3.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
|
||||
mol representation CPK
|
||||
mol color Name
|
||||
mol material Opaque
|
||||
mol addrep top
|
||||
|
||||
###################################################################
|
||||
|
||||
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
animate delete beg 0 end 0 skip 0 4
|
||||
mol addfile dcd/H2_4.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
|
||||
mol representation CPK
|
||||
mol color Name
|
||||
mol material Opaque
|
||||
mol addrep top
|
||||
|
||||
###################################################################
|
||||
|
||||
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
animate delete beg 0 end 0 skip 0 5
|
||||
mol addfile dcd/H2_5.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
|
||||
mol representation CPK
|
||||
mol color Name
|
||||
mol material Opaque
|
||||
mol addrep top
|
||||
|
||||
###################################################################
|
||||
|
||||
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
animate delete beg 0 end 0 skip 0 6
|
||||
mol addfile dcd/H2_6.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
|
||||
mol representation CPK
|
||||
mol color Name
|
||||
mol material Opaque
|
||||
mol addrep top
|
||||
|
||||
###################################################################
|
||||
|
||||
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
animate delete beg 0 end 0 skip 0 7
|
||||
mol addfile dcd/H2_7.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
|
||||
|
||||
mol representation CPK
|
||||
mol color Name
|
||||
mol material Opaque
|
||||
mol addrep top
|
||||
|
||||
|
||||
|
||||
display projection Orthographic
|
||||
display depthcue off
|
||||
rotate x by -90.0
|
||||
|
|
@ -0,0 +1,31 @@
|
|||
variable ibead uloop 8 pad
|
||||
|
||||
units real
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
|
||||
pair_style lj/charmm/coul/long 11 12
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
|
||||
read_data system.data
|
||||
#read_restart restart/system_${ibead}.rest1
|
||||
special_bonds charmm
|
||||
|
||||
fix 1 all quantum method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp pe etotal
|
||||
timestep 0.08
|
||||
|
||||
restart 100 restart/system_${ibead}.rest1 restart/system_${ibead}.rest2
|
||||
|
||||
group prot id <= 256
|
||||
dump 1 prot dcd 100 dcd/prot_${ibead}.dcd
|
||||
|
||||
run 2000000
|
||||
|
|
@ -0,0 +1 @@
|
|||
mpirun -np 8 lmp_mpi -partition 8x1 -in in.scp -log logfile/log.lammps -screen screen/screen
|
||||
File diff suppressed because it is too large
Load Diff
Loading…
Reference in New Issue