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replaced non ascii parameters (-)
1 parent 1de9676 commit 40da661

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7 files changed

+8434
-8434
lines changed

files/tutorial4/groups.inc

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
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group H2O type O H
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group Na type Na+
8-
group Cl type Cl
8+
group Cl type Cl-
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group ions union Na Cl
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group fluid union H2O ions
1111

files/tutorial4/parameters.inc

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -6,15 +6,15 @@
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mass O 15.9994
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mass H 1.008
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mass Na+ 22.990
9-
mass Cl 35.453
9+
mass Cl- 35.453
1010
mass WALL 26.9815
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pair_coeff O O 0.185199 3.1589
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pair_coeff H H 0.0 1.0
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pair_coeff Na+ Na+ 0.04690 2.4299
15-
pair_coeff Cl Cl 0.1500 4.04470
15+
pair_coeff Cl- Cl- 0.1500 4.04470
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pair_coeff WALL WALL 11.697 2.574
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pair_coeff O WALL 0.4 2.86645
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bond_coeff OH 0 0.9572
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angle_coeff HOH 0 104.52
19+
bond_coeff O-H 0 0.9572
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angle_coeff H-O-H 0 104.52

files/tutorial4/solution/create.lmp

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -8,35 +8,35 @@ units real
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atom_style full
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bond_style harmonic
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angle_style harmonic
11-
pair_style lj/cut/tip4p/long O H OH H−O−H 0.1546 12.0
12-
kspace_style pppm/tip4p 1.0e5
11+
pair_style lj/cut/tip4p/long O H O-H H-O-H 0.1546 12.0
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kspace_style pppm/tip4p 1.0e-5
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kspace_modify slab 3.0
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lattice fcc 4.04
16-
region box block 3 3 3 3 5 5
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region box block -3 3 -3 3 -5 5
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create_box 5 box &
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bond/types 1 &
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angle/types 1 &
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extra/bond/per/atom 2 &
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extra/angle/per/atom 1 &
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extra/special/per/atom 2
23-
labelmap atom 1 O 2 H 3 Na+ 4 Cl 5 WALL
24-
labelmap bond 1 OH
25-
labelmap angle 1 H−O−H
23+
labelmap atom 1 O 2 H 3 Na+ 4 Cl- 5 WALL
24+
labelmap bond 1 O-H
25+
labelmap angle 1 H-O-H
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27-
region rbotwall block 3 3 3 3 −4 −3
28-
region rtopwall block 3 3 3 3 3 4
27+
region rbotwall block -3 3 -3 3 -4 -3
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region rtopwall block -3 3 -3 3 3 4
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region rwall union 2 rbotwall rtopwall
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create_atoms WALL region rwall
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32-
region rliquid block INF INF INF INF 2 2
32+
region rliquid block INF INF INF INF -2 2
3333
molecule h2omol water.mol
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create_atoms 0 region rliquid mol h2omol 482793
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create_atoms Na+ random 15 5802 rliquid overlap 0.3 maxtry 500
37-
create_atoms Cl random 15 9012 rliquid overlap 0.3 maxtry 500
37+
create_atoms Cl- random 15 9012 rliquid overlap 0.3 maxtry 500
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set type Na+ charge 1
39-
set type Cl charge 1
39+
set type Cl- charge -1
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4141
include parameters.inc
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include groups.inc
@@ -49,7 +49,7 @@ dump_modify mydmp backcolor white &
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acolor O red adiam O 2 &
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acolor H white adiam H 1 &
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acolor Na+ blue adiam Na+ 2.5 &
52-
acolor Cl cyan adiam Cl 3 &
52+
acolor Cl- cyan adiam Cl- 3 &
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acolor WALL gray adiam WALL 3
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run 0

files/tutorial4/solution/equilibrate.data

Lines changed: 4572 additions & 4572 deletions
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files/tutorial4/solution/equilibrate.lmp

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -8,8 +8,8 @@ units real
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atom_style full
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bond_style harmonic
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angle_style harmonic
11-
pair_style lj/cut/tip4p/long O H OH H−O−H 0.1546 12.0
12-
kspace_style pppm/tip4p 1.0e5
11+
pair_style lj/cut/tip4p/long O H O-H H-O-H 0.1546 12.0
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kspace_style pppm/tip4p 1.0e-5
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kspace_modify slab 3.0
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read_data minimize.data
@@ -18,7 +18,7 @@ include parameters.inc
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include groups.inc
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2020
fix mynvt all nvt temp 300 300 100
21-
fix myshk H2O shake 1.0e5 200 0 b OH a H−O−H
21+
fix myshk H2O shake 1.0e-5 200 0 b O-H a H-O-H
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fix myrct all recenter NULL NULL 0
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timestep 1.0
2424

@@ -28,12 +28,12 @@ dump_modify mydmp backcolor white &
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acolor O red adiam O 2 &
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acolor H white adiam H 1 &
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acolor Na+ blue adiam Na+ 2.5 &
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acolor Cl cyan adiam Cl 3 &
31+
acolor Cl- cyan adiam Cl- 3 &
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acolor WALL gray adiam WALL 3
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3434
variable walltopz equal xcm(walltop,z)
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variable wallbotz equal xcm(wallbot,z)
36-
variable deltaz equal v_walltopzv_wallbotz
36+
variable deltaz equal v_walltopz-v_wallbotz
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thermo 250
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thermo_style custom step temp etotal press v_deltaz

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