How to solve "Non-numeric atom coords - simulation unstable"

LAMMPS LAMMPS Beginners
, ,
1

Dear All,

I am creating a CNT writing my own mathematica code, and I am exporting the data file to be read by lammps. Running my code I am getting the Error:

“Non-numeric atom coords - simulation unstable”

Reading the answers on MATSCI for the same error I know that this error can be caused by atoms being too close together and the forces too large. So I tried to increase the distance between the atoms (even more than the lattice constant of the CNT), but I am still getting the same error. (I am not sure which part of my code do I need to provide to give more explanation, because I guess the problem is with the data file).

My questions are
-Is there any suggestions about the other possible causes of the error ?
-I am using atomic style hybrid edpd full. Do you have suggestions about an estimate atom (bead) distance for CNT that result in reosonable forces?

Thanks a lot.

2

If there is a problem with your algorithm that produces atoms on exactly overlapping positions, then changing the C-C atom distance won’t address it.

As has been mentioned multiple times, the easiest way to test from within LAMMPS if there are close contacts is to add a command like the following and monitor the output/log:

delete_atoms overlap 0.1 all all

If this deletes atoms, you have close contacts.

Please note that close contacts is only one possible reason (albeit the most common one).

For the best kind of report and the best chance of getting competent help, you should create a special test input deck with a very small system (so it can run fast and is easy to debug) that still reproduces the issue and then provide all required input files and the corresponding log file from your machine.

3

Dear akohlmey, thank you for your fast response. I followed your instructions when you mentioned using the delete_atoms overlap on perivious asking questions and I was also getting the same error as them, in which some bonds where getting deleted…I know there is something wrong that I am getting large forces, but I cannot figure out what can be the issue (if its not the distances that causes atoms to be very close together) to fix it.

I am trying to write a smaller version of my code, to provide here, but meanwhile I thought I tell you what my issue is so far. I will post it as soon as I get it to work

4

For now it would already be a big help if you could provide the log file with the delete_atoms command included.

5

units lj
dimension 3
boundary p p p
neigh_modify one 10000 delay 0 check yes

change neighbor list parameters to avoid dangerous builds

atom_style hybrid edpd full
bond_style harmonic
angle_style harmonic

System definition

region edpd block -20 20 -20 20 -20 20 units box
pair_style edpd 1.6 9872598

read_data tubete.dat
Reading data file …
orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 1 by 1 MPI processor grid
reading atoms …
53 atoms
scanning bonds …
4 = max bonds/atom
scanning angles …
8 = max angles/atom
reading bonds …
138 bonds
reading angles …
332 angles
Finding 1-2 1-3 1-4 neighbors …
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
6 = max # of 1-2 neighbors
30 = max # of 1-3 neighbors
180 = max # of 1-4 neighbors
36 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.006 seconds

create_atoms 2 random 1000 276438 NULL
Created 1000 atoms
using lattice units in orthogonal box = (-10 -10 -10) to (10 10 10)
create_atoms CPU = 0.001 seconds

comm_modify vel yes

delete_atoms overlap 0.3 all all
System init for delete_atoms …
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info …
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 1.88
ghost atom cutoff = 1.88
binsize = 0.94, bins = 22 22 22
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) pair edpd, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff 1.8800000000000001 is shorter than a bond length based estimate of 2.3999999999999995. This may lead to errors. (src/comm.cpp:727)
WARNING: Ignoring ‘compress yes’ for molecular system (src/delete_atoms.cpp:140)
Deleted 9 atoms, new total = 1044

#grouping

group cnt type 1
51 atoms in group cnt
group liquid type 2
993 atoms in group liquid

mass 1 1
mass 2 12
set atom * edpd/temp 1.0
Setting atom values …
1044 settings made for edpd/temp
set atom * edpd/cv 1.0E5
Setting atom values …
1044 settings made for edpd/cv

#bond_coeff 1 80.0 1.2
#angle_coeff 1 300.0 107.0 50.0 3.0

#pair_coeff * * 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 # power 10.54 -3.66 3.44 -4.10 # kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes

comm_modify vel yes

velocity all create 0.4 432982 loop local dist gaussian

#fix 1 cnt property/atom mol
#fix rigid cnt rigid molecule

fix mvv all mvv/edpd 0.5
fix cnt cnt edpd/source cuboid -50 -30 -21 100.0 60.0 42.0 0.4
#fix liquid liquid edpd/source cuboid -50 -30 -21 100.0 60.0 42.0 -0.01

timestep 0.01
run 1000

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

Your simulation uses code contributions which should be cited:

  • pair edpd command:

@Article{ZLi2014_JCP,
author = {Li, Z. and Tang, Y.-H. and Lei, H. and Caswell, B. and Karniadakis, G.E.},
title = {Energy-conserving dissipative particle dynamics with temperature-dependent properties},
journal = {Journal of Computational Physics},
year = {2014},
volume = {265},
pages = {113–127}
}

@Article{ZLi2015_CC,
author = {Li, Z. and Tang, Y.-H. and Li, X. and Karniadakis, G.E.},
title = {Mesoscale modeling of phase transition dynamics of thermoresponsive polymers},
journal = {Chemical Communications},
year = {2015},
volume = {51},
pages = {11038–11040}
}

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

Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info …
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 1.88
ghost atom cutoff = 1.88
binsize = 0.94, bins = 22 22 22
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair edpd, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff 1.8800000000000001 is shorter than a bond length based estimate of 2.3999999999999995. This may lead to errors. (src/comm.cpp:727)
ERROR on proc 0: Bond atom missing in image check (src/domain.cpp:799)
Last command: run 1000

6

How to attach a file here? there is no choice to upload the file. I copied and pasted it for now.

7

Trying delete_atoms overlap 0.1 all all:

units lj
dimension 3
boundary p p p
neigh_modify one 10000 delay 0 check yes

change neighbor list parameters to avoid dangerous builds

atom_style hybrid edpd full
bond_style harmonic
angle_style harmonic

System definition

region edpd block -20 20 -20 20 -20 20 units box
pair_style edpd 1.6 9872598

read_data tubete.dat
Reading data file …
orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 1 by 1 MPI processor grid
reading atoms …
53 atoms
scanning bonds …
4 = max bonds/atom
scanning angles …
8 = max angles/atom
reading bonds …
138 bonds
reading angles …
332 angles
Finding 1-2 1-3 1-4 neighbors …
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
6 = max # of 1-2 neighbors
30 = max # of 1-3 neighbors
180 = max # of 1-4 neighbors
36 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds

create_atoms 2 random 1000 276438 NULL
Created 1000 atoms
using lattice units in orthogonal box = (-10 -10 -10) to (10 10 10)
create_atoms CPU = 0.000 seconds

comm_modify vel yes

delete_atoms overlap 0.1 all all
System init for delete_atoms …
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info …
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 1.88
ghost atom cutoff = 1.88
binsize = 0.94, bins = 22 22 22
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) pair edpd, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff 1.8800000000000001 is shorter than a bond length based estimate of 2.3999999999999995. This may lead to errors. (src/comm.cpp:727)
WARNING: Ignoring ‘compress yes’ for molecular system (src/delete_atoms.cpp:140)
Deleted 0 atoms, new total = 1053

#grouping

group cnt type 1
53 atoms in group cnt
group liquid type 2
1000 atoms in group liquid

mass 1 1
mass 2 12
set atom * edpd/temp 1.0
Setting atom values …
1053 settings made for edpd/temp
set atom * edpd/cv 1.0E5
Setting atom values …
1053 settings made for edpd/cv

#bond_coeff 1 80.0 1.2
#angle_coeff 1 300.0 107.0 50.0 3.0

#pair_coeff * * 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 # power 10.54 -3.66 3.44 -4.10 # kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes

comm_modify vel yes

velocity all create 0.4 432982 loop local dist gaussian

#fix 1 cnt property/atom mol
#fix rigid cnt rigid molecule

fix mvv all mvv/edpd 0.5
fix cnt cnt edpd/source cuboid -50 -30 -21 100.0 60.0 42.0 0.4
#fix liquid liquid edpd/source cuboid -50 -30 -21 100.0 60.0 42.0 -0.01

timestep 0.01
run 1000

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

Your simulation uses code contributions which should be cited:

  • pair edpd command:

@Article{ZLi2014_JCP,
author = {Li, Z. and Tang, Y.-H. and Lei, H. and Caswell, B. and Karniadakis, G.E.},
title = {Energy-conserving dissipative particle dynamics with temperature-dependent properties},
journal = {Journal of Computational Physics},
year = {2014},
volume = {265},
pages = {113–127}
}

@Article{ZLi2015_CC,
author = {Li, Z. and Tang, Y.-H. and Li, X. and Karniadakis, G.E.},
title = {Mesoscale modeling of phase transition dynamics of thermoresponsive polymers},
journal = {Chemical Communications},
year = {2015},
volume = {51},
pages = {11038–11040}
}

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

Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info …
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 1.88
ghost atom cutoff = 1.88
binsize = 0.94, bins = 22 22 22
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair edpd, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff 1.8800000000000001 is shorter than a bond length based estimate of 2.3999999999999995. This may lead to errors. (src/comm.cpp:727)
Per MPI rank memory allocation (min/avg/max) = 11.83 | 11.83 | 11.83 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.4 1.7600618 98.868714 101.22821 1.7862176
ERROR on proc 0: Non-numeric atom coords - simulation unstable (src/OPENMP/domain_omp.cpp:58)
Last command: run 1000

8

One important piece of information is missing from your log files, the LAMMPS version!

So you have at least 9 atoms that are quite close to each other.

Also, you may need to set comm_modify cutoff to a value of 2.5 or more in order to avoid issues with “lost bond atoms”. Since your pair style cutoff is rather short in comparison and thus you would be missing ghost atoms.

The next step to narrow down your problems would be to set up a simulation for each subsystem separately and see if one of them already produces the instability or both.

Another issue would be to avoid edpd and use plain dpd instead.

Basically, the process of debugging is to stepwise move from a know-to-work system to the desired target setup. When doing this carefully, you can identify at which step things go south and that will tell you what kind of solutions to look for. You just jumped ahead (and then jumped too far) and now there are too many factors to be able to tell which is causing you problems (not to mention that it might be multiple).

So those close contacts have a distance between 0.1 and 0.3 sigma.

9

Thank you so much. My LAMMPS version is LAMMPS (23 Jun 2022). I have two types of atoms, one is the water atoms which I create in the input file and the CNT which I read from a data file. I did the subsystem debugging and the problem is just the CNT (not water). Is that what you mean by setting up a subsystem simulation for each system? . I have one more question. Suppose by try and error I figured out what is the exact distance of the close contact atoms. How should I fix it? I mean if those atoms are from CNT, I do not want to delete them because I want my CNT to maintain its cylindrical shape.

10

There is no trial and error needed. Write out all coordinates to a dump file (sorted by ID!) before the delete_atoms command (with 0.3 sigma) and then after. By comparing the two files, you can identify which atoms are one half of a problematic pair and then you should be able to determine why they are so close. Everything else follows from there. This is just common sense and standard simulation procedure. I don’t know enough to your research and details of your simulation to be able to give you specific advice. If needed, you should ask your adviser/tutor for assistance with these procedures. Those are no longer LAMMPS issues and thus off-topic for this forum category.

11

[quote=“nema9210, post:9, topic:46284”]
LAMMPS (23 Jun 2022)

Hello Akohlmey

I am adding a smaller version of my code pluse the data file for which I am getting the same “Non numeric atom coord”. What I did I grabbed an example from edpd and added a CNT to it. in this versin if comment out the “mvv all mvv/edpd 0.2” it runs without any error. but when I have the command I am getting the “Non numeric atom coord” error.

I think that there is no problem with my CNT data file. I mean in case if the structure, number of bonds and angles.

This is maybe more of a physics question but do youthink the problem can also arise from the wrong edpd_cv value ?

I am adding the example of the program and data version to the above question in another comments

12 
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem       ###
### using energy-conserving DPD (eDPD) simulation                    ###
###                                                                  ### 
### Created  : Zhen Li ([email protected])                           ### 
###            Division of Applied Mathematics, Brown University.    ###
###                                                                  ###
### mDPD system setup follows Fig.12 in the publication:             ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis.      ###
### "Energy-conserving dissipative particle dynamics with            ###
### temperature-dependent properties". J. Comput. Phys.,             ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003               ###
########################################################################
units 		        lj
dimension	        3
boundary	        p p p
neighbor	        0.2 bin
neigh_modify            every 1 delay 0 check yes

atom_style	        hybrid edpd full
bond_style              harmonic
angle_style             harmonic

region     edpd     block -20 20 -20 20 -10 10 units box
pair_style          edpd 1.58 9872598 


read_data           tube1.dat 

create_atoms        2 random 16000 276438 NULL

set                 atom * edpd/temp 5.0
set                 atom * edpd/cv   0.2

#comm_modify vel yes


#delete_atoms overlap 0.1 all all

#grouping

group		cnt		type	1
group           liquid          type    2


compute             mythermo all temp
thermo              100
thermo_modify       temp mythermo
thermo_modify       flush yes

comm_modify vel yes

velocity            all create 1.0 432982 loop local dist gaussian

fix          mvv     all mvv/edpd 0.2
fix          cnt   all edpd/source cuboid -20  40 -20 40.0 -10 20.0  0.01
fix          liquid   all edpd/source cuboid -20  40 -20 40.0 -10 20.0 -0.01

timestep            0.01
run                 500
reset_timestep      0

compute     temp    all edpd/temp/atom
compute     ccT     all chunk/atom bin/1d y 0.0 1.0 
fix         stat    all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile

run                 500
13 
LAMMPS data file via Mathematica 


252	atoms
492	bonds
960	angles
0	dihedrals
0	impropers
2	atom types
1	bond types
1	angle types
0	dihedral types
0	improper types

-10.	10.	xlo xhi
-10.	10.	ylo yhi
-10.	10.	zlo zhi

Masses

1	12
2	7

PairIJ Coeffs # edpd

1	1	10.75	4.5	0.41	1.58	1.42	2.	1.58
2	2	10.75	4.5	0.41	1.58	1.42	2.	1.58
1	2	10.75	4.5	0.41	1.58	1.42	2.	1.58

Bond Coeffs # harmonic

1	469	1.4

Angle Coeffs # harmonic

1	400.	90.

Atoms # hybrid

1	1	0.4135	0.23873	-4.75	5	0.2	1	-1
2	1	0.4135	0.23873	-4.5	5	0.2	1	-1
3	1	0.4135	0.23873	-4.25	5	0.2	1	-1
4	1	0.4135	0.23873	-4.	5	0.2	1	-1
5	1	0.4135	0.23873	-3.75	5	0.2	1	-1
6	1	0.4135	0.23873	-3.5	5	0.2	1	-1
7	1	0.4135	0.23873	-3.25	5	0.2	1	-1
8	1	0.4135	0.23873	-3.	5	0.2	1	-1
9	1	0.4135	0.23873	-2.75	5	0.2	1	-1
10	1	0.4135	0.23873	-2.5	5	0.2	1	-1
11	1	0.4135	0.23873	-2.25	5	0.2	1	-1
12	1	0.4135	0.23873	-2.	5	0.2	1	-1
13	1	0.4135	0.23873	-1.75	5	0.2	1	-1
14	1	0.4135	0.23873	-1.5	5	0.2	1	-1
15	1	0.4135	0.23873	-1.25	5	0.2	1	-1
16	1	0.4135	0.23873	-1.	5	0.2	1	-1
17	1	0.4135	0.23873	-0.75	5	0.2	1	-1
18	1	0.4135	0.23873	-0.5	5	0.2	1	-1
19	1	0.4135	0.23873	-0.25	5	0.2	1	-1
20	1	0.4135	0.23873	0.	5	0.2	1	-1
21	1	0.4135	0.23873	0.25	5	0.2	1	-1
22	1	0.23873	0.4135	-4.75	5	0.2	1	-1
23	1	0.23873	0.4135	-4.5	5	0.2	1	-1
24	1	0.23873	0.4135	-4.25	5	0.2	1	-1
25	1	0.23873	0.4135	-4.	5	0.2	1	-1
26	1	0.23873	0.4135	-3.75	5	0.2	1	-1
27	1	0.23873	0.4135	-3.5	5	0.2	1	-1
28	1	0.23873	0.4135	-3.25	5	0.2	1	-1
29	1	0.23873	0.4135	-3.	5	0.2	1	-1
30	1	0.23873	0.4135	-2.75	5	0.2	1	-1
31	1	0.23873	0.4135	-2.5	5	0.2	1	-1
32	1	0.23873	0.4135	-2.25	5	0.2	1	-1
33	1	0.23873	0.4135	-2.	5	0.2	1	-1
34	1	0.23873	0.4135	-1.75	5	0.2	1	-1
35	1	0.23873	0.4135	-1.5	5	0.2	1	-1
36	1	0.23873	0.4135	-1.25	5	0.2	1	-1
37	1	0.23873	0.4135	-1.	5	0.2	1	-1
38	1	0.23873	0.4135	-0.75	5	0.2	1	-1
39	1	0.23873	0.4135	-0.5	5	0.2	1	-1
40	1	0.23873	0.4135	-0.25	5	0.2	1	-1
41	1	0.23873	0.4135	0.	5	0.2	1	-1
42	1	0.23873	0.4135	0.25	5	0.2	1	-1
43	1	0.	0.47746	-4.75	5	0.2	1	-1
44	1	0.	0.47746	-4.5	5	0.2	1	-1
45	1	0.	0.47746	-4.25	5	0.2	1	-1
46	1	0.	0.47746	-4.	5	0.2	1	-1
47	1	0.	0.47746	-3.75	5	0.2	1	-1
48	1	0.	0.47746	-3.5	5	0.2	1	-1
49	1	0.	0.47746	-3.25	5	0.2	1	-1
50	1	0.	0.47746	-3.	5	0.2	1	-1
51	1	0.	0.47746	-2.75	5	0.2	1	-1
52	1	0.	0.47746	-2.5	5	0.2	1	-1
53	1	0.	0.47746	-2.25	5	0.2	1	-1
54	1	0.	0.47746	-2.	5	0.2	1	-1
55	1	0.	0.47746	-1.75	5	0.2	1	-1
56	1	0.	0.47746	-1.5	5	0.2	1	-1
57	1	0.	0.47746	-1.25	5	0.2	1	-1
58	1	0.	0.47746	-1.	5	0.2	1	-1
59	1	0.	0.47746	-0.75	5	0.2	1	-1
60	1	0.	0.47746	-0.5	5	0.2	1	-1
61	1	0.	0.47746	-0.25	5	0.2	1	-1
62	1	0.	0.47746	0.	5	0.2	1	-1
63	1	0.	0.47746	0.25	5	0.2	1	-1
64	1	-0.23873	0.4135	-4.75	5	0.2	1	-1
65	1	-0.23873	0.4135	-4.5	5	0.2	1	-1
66	1	-0.23873	0.4135	-4.25	5	0.2	1	-1
67	1	-0.23873	0.4135	-4.	5	0.2	1	-1
68	1	-0.23873	0.4135	-3.75	5	0.2	1	-1
69	1	-0.23873	0.4135	-3.5	5	0.2	1	-1
70	1	-0.23873	0.4135	-3.25	5	0.2	1	-1
71	1	-0.23873	0.4135	-3.	5	0.2	1	-1
72	1	-0.23873	0.4135	-2.75	5	0.2	1	-1
73	1	-0.23873	0.4135	-2.5	5	0.2	1	-1
74	1	-0.23873	0.4135	-2.25	5	0.2	1	-1
75	1	-0.23873	0.4135	-2.	5	0.2	1	-1
76	1	-0.23873	0.4135	-1.75	5	0.2	1	-1
77	1	-0.23873	0.4135	-1.5	5	0.2	1	-1
78	1	-0.23873	0.4135	-1.25	5	0.2	1	-1
79	1	-0.23873	0.4135	-1.	5	0.2	1	-1
80	1	-0.23873	0.4135	-0.75	5	0.2	1	-1
81	1	-0.23873	0.4135	-0.5	5	0.2	1	-1
82	1	-0.23873	0.4135	-0.25	5	0.2	1	-1
83	1	-0.23873	0.4135	0.	5	0.2	1	-1
84	1	-0.23873	0.4135	0.25	5	0.2	1	-1
85	1	-0.4135	0.23873	-4.75	5	0.2	1	-1
86	1	-0.4135	0.23873	-4.5	5	0.2	1	-1
87	1	-0.4135	0.23873	-4.25	5	0.2	1	-1
88	1	-0.4135	0.23873	-4.	5	0.2	1	-1
89	1	-0.4135	0.23873	-3.75	5	0.2	1	-1
90	1	-0.4135	0.23873	-3.5	5	0.2	1	-1
91	1	-0.4135	0.23873	-3.25	5	0.2	1	-1
92	1	-0.4135	0.23873	-3.	5	0.2	1	-1
93	1	-0.4135	0.23873	-2.75	5	0.2	1	-1
94	1	-0.4135	0.23873	-2.5	5	0.2	1	-1
95	1	-0.4135	0.23873	-2.25	5	0.2	1	-1
96	1	-0.4135	0.23873	-2.	5	0.2	1	-1
97	1	-0.4135	0.23873	-1.75	5	0.2	1	-1
98	1	-0.4135	0.23873	-1.5	5	0.2	1	-1
99	1	-0.4135	0.23873	-1.25	5	0.2	1	-1
100	1	-0.4135	0.23873	-1.	5	0.2	1	-1
101	1	-0.4135	0.23873	-0.75	5	0.2	1	-1
102	1	-0.4135	0.23873	-0.5	5	0.2	1	-1
103	1	-0.4135	0.23873	-0.25	5	0.2	1	-1
104	1	-0.4135	0.23873	0.	5	0.2	1	-1
105	1	-0.4135	0.23873	0.25	5	0.2	1	-1
106	1	-0.47746	0.	-4.75	5	0.2	1	-1
107	1	-0.47746	0.	-4.5	5	0.2	1	-1
108	1	-0.47746	0.	-4.25	5	0.2	1	-1
109	1	-0.47746	0.	-4.	5	0.2	1	-1
110	1	-0.47746	0.	-3.75	5	0.2	1	-1
111	1	-0.47746	0.	-3.5	5	0.2	1	-1
112	1	-0.47746	0.	-3.25	5	0.2	1	-1
113	1	-0.47746	0.	-3.	5	0.2	1	-1
114	1	-0.47746	0.	-2.75	5	0.2	1	-1
115	1	-0.47746	0.	-2.5	5	0.2	1	-1
116	1	-0.47746	0.	-2.25	5	0.2	1	-1
117	1	-0.47746	0.	-2.	5	0.2	1	-1
118	1	-0.47746	0.	-1.75	5	0.2	1	-1
119	1	-0.47746	0.	-1.5	5	0.2	1	-1
120	1	-0.47746	0.	-1.25	5	0.2	1	-1
121	1	-0.47746	0.	-1.	5	0.2	1	-1
122	1	-0.47746	0.	-0.75	5	0.2	1	-1
123	1	-0.47746	0.	-0.5	5	0.2	1	-1
124	1	-0.47746	0.	-0.25	5	0.2	1	-1
125	1	-0.47746	0.	0.	5	0.2	1	-1
126	1	-0.47746	0.	0.25	5	0.2	1	-1
127	1	-0.4135	-0.23873	-4.75	5	0.2	1	-1
128	1	-0.4135	-0.23873	-4.5	5	0.2	1	-1
129	1	-0.4135	-0.23873	-4.25	5	0.2	1	-1
130	1	-0.4135	-0.23873	-4.	5	0.2	1	-1
131	1	-0.4135	-0.23873	-3.75	5	0.2	1	-1
132	1	-0.4135	-0.23873	-3.5	5	0.2	1	-1
133	1	-0.4135	-0.23873	-3.25	5	0.2	1	-1
134	1	-0.4135	-0.23873	-3.	5	0.2	1	-1
135	1	-0.4135	-0.23873	-2.75	5	0.2	1	-1
136	1	-0.4135	-0.23873	-2.5	5	0.2	1	-1
137	1	-0.4135	-0.23873	-2.25	5	0.2	1	-1
138	1	-0.4135	-0.23873	-2.	5	0.2	1	-1
139	1	-0.4135	-0.23873	-1.75	5	0.2	1	-1
140	1	-0.4135	-0.23873	-1.5	5	0.2	1	-1
141	1	-0.4135	-0.23873	-1.25	5	0.2	1	-1
142	1	-0.4135	-0.23873	-1.	5	0.2	1	-1
143	1	-0.4135	-0.23873	-0.75	5	0.2	1	-1
144	1	-0.4135	-0.23873	-0.5	5	0.2	1	-1
145	1	-0.4135	-0.23873	-0.25	5	0.2	1	-1
146	1	-0.4135	-0.23873	0.	5	0.2	1	-1
147	1	-0.4135	-0.23873	0.25	5	0.2	1	-1
148	1	-0.23873	-0.4135	-4.75	5	0.2	1	-1
149	1	-0.23873	-0.4135	-4.5	5	0.2	1	-1
150	1	-0.23873	-0.4135	-4.25	5	0.2	1	-1
151	1	-0.23873	-0.4135	-4.	5	0.2	1	-1
152	1	-0.23873	-0.4135	-3.75	5	0.2	1	-1
153	1	-0.23873	-0.4135	-3.5	5	0.2	1	-1
154	1	-0.23873	-0.4135	-3.25	5	0.2	1	-1
155	1	-0.23873	-0.4135	-3.	5	0.2	1	-1
156	1	-0.23873	-0.4135	-2.75	5	0.2	1	-1
157	1	-0.23873	-0.4135	-2.5	5	0.2	1	-1
158	1	-0.23873	-0.4135	-2.25	5	0.2	1	-1
159	1	-0.23873	-0.4135	-2.	5	0.2	1	-1
160	1	-0.23873	-0.4135	-1.75	5	0.2	1	-1
161	1	-0.23873	-0.4135	-1.5	5	0.2	1	-1
162	1	-0.23873	-0.4135	-1.25	5	0.2	1	-1
163	1	-0.23873	-0.4135	-1.	5	0.2	1	-1
164	1	-0.23873	-0.4135	-0.75	5	0.2	1	-1
165	1	-0.23873	-0.4135	-0.5	5	0.2	1	-1
166	1	-0.23873	-0.4135	-0.25	5	0.2	1	-1
167	1	-0.23873	-0.4135	0.	5	0.2	1	-1
168	1	-0.23873	-0.4135	0.25	5	0.2	1	-1
169	1	0.	-0.47746	-4.75	5	0.2	1	-1
170	1	0.	-0.47746	-4.5	5	0.2	1	-1
171	1	0.	-0.47746	-4.25	5	0.2	1	-1
172	1	0.	-0.47746	-4.	5	0.2	1	-1
173	1	0.	-0.47746	-3.75	5	0.2	1	-1
174	1	0.	-0.47746	-3.5	5	0.2	1	-1
175	1	0.	-0.47746	-3.25	5	0.2	1	-1
176	1	0.	-0.47746	-3.	5	0.2	1	-1
177	1	0.	-0.47746	-2.75	5	0.2	1	-1
178	1	0.	-0.47746	-2.5	5	0.2	1	-1
179	1	0.	-0.47746	-2.25	5	0.2	1	-1
180	1	0.	-0.47746	-2.	5	0.2	1	-1
181	1	0.	-0.47746	-1.75	5	0.2	1	-1
182	1	0.	-0.47746	-1.5	5	0.2	1	-1
183	1	0.	-0.47746	-1.25	5	0.2	1	-1
184	1	0.	-0.47746	-1.	5	0.2	1	-1
185	1	0.	-0.47746	-0.75	5	0.2	1	-1
186	1	0.	-0.47746	-0.5	5	0.2	1	-1
187	1	0.	-0.47746	-0.25	5	0.2	1	-1
188	1	0.	-0.47746	0.	5	0.2	1	-1
189	1	0.	-0.47746	0.25	5	0.2	1	-1
190	1	0.23873	-0.4135	-4.75	5	0.2	1	-1
191	1	0.23873	-0.4135	-4.5	5	0.2	1	-1
192	1	0.23873	-0.4135	-4.25	5	0.2	1	-1
193	1	0.23873	-0.4135	-4.	5	0.2	1	-1
194	1	0.23873	-0.4135	-3.75	5	0.2	1	-1
195	1	0.23873	-0.4135	-3.5	5	0.2	1	-1
196	1	0.23873	-0.4135	-3.25	5	0.2	1	-1
197	1	0.23873	-0.4135	-3.	5	0.2	1	-1
198	1	0.23873	-0.4135	-2.75	5	0.2	1	-1
199	1	0.23873	-0.4135	-2.5	5	0.2	1	-1
200	1	0.23873	-0.4135	-2.25	5	0.2	1	-1
201	1	0.23873	-0.4135	-2.	5	0.2	1	-1
202	1	0.23873	-0.4135	-1.75	5	0.2	1	-1
203	1	0.23873	-0.4135	-1.5	5	0.2	1	-1
204	1	0.23873	-0.4135	-1.25	5	0.2	1	-1
205	1	0.23873	-0.4135	-1.	5	0.2	1	-1
206	1	0.23873	-0.4135	-0.75	5	0.2	1	-1
207	1	0.23873	-0.4135	-0.5	5	0.2	1	-1
208	1	0.23873	-0.4135	-0.25	5	0.2	1	-1
209	1	0.23873	-0.4135	0.	5	0.2	1	-1
210	1	0.23873	-0.4135	0.25	5	0.2	1	-1
211	1	0.4135	-0.23873	-4.75	5	0.2	1	-1
212	1	0.4135	-0.23873	-4.5	5	0.2	1	-1
213	1	0.4135	-0.23873	-4.25	5	0.2	1	-1
214	1	0.4135	-0.23873	-4.	5	0.2	1	-1
215	1	0.4135	-0.23873	-3.75	5	0.2	1	-1
216	1	0.4135	-0.23873	-3.5	5	0.2	1	-1
217	1	0.4135	-0.23873	-3.25	5	0.2	1	-1
218	1	0.4135	-0.23873	-3.	5	0.2	1	-1
219	1	0.4135	-0.23873	-2.75	5	0.2	1	-1
220	1	0.4135	-0.23873	-2.5	5	0.2	1	-1
221	1	0.4135	-0.23873	-2.25	5	0.2	1	-1
222	1	0.4135	-0.23873	-2.	5	0.2	1	-1
223	1	0.4135	-0.23873	-1.75	5	0.2	1	-1
224	1	0.4135	-0.23873	-1.5	5	0.2	1	-1
225	1	0.4135	-0.23873	-1.25	5	0.2	1	-1
226	1	0.4135	-0.23873	-1.	5	0.2	1	-1
227	1	0.4135	-0.23873	-0.75	5	0.2	1	-1
228	1	0.4135	-0.23873	-0.5	5	0.2	1	-1
229	1	0.4135	-0.23873	-0.25	5	0.2	1	-1
230	1	0.4135	-0.23873	0.	5	0.2	1	-1
231	1	0.4135	-0.23873	0.25	5	0.2	1	-1
232	1	0.47746	0.	-4.75	5	0.2	1	-1
233	1	0.47746	0.	-4.5	5	0.2	1	-1
234	1	0.47746	0.	-4.25	5	0.2	1	-1
235	1	0.47746	0.	-4.	5	0.2	1	-1
236	1	0.47746	0.	-3.75	5	0.2	1	-1
237	1	0.47746	0.	-3.5	5	0.2	1	-1
238	1	0.47746	0.	-3.25	5	0.2	1	-1
239	1	0.47746	0.	-3.	5	0.2	1	-1
240	1	0.47746	0.	-2.75	5	0.2	1	-1
241	1	0.47746	0.	-2.5	5	0.2	1	-1
242	1	0.47746	0.	-2.25	5	0.2	1	-1
243	1	0.47746	0.	-2.	5	0.2	1	-1
244	1	0.47746	0.	-1.75	5	0.2	1	-1
245	1	0.47746	0.	-1.5	5	0.2	1	-1
246	1	0.47746	0.	-1.25	5	0.2	1	-1
247	1	0.47746	0.	-1.	5	0.2	1	-1
248	1	0.47746	0.	-0.75	5	0.2	1	-1
249	1	0.47746	0.	-0.5	5	0.2	1	-1
250	1	0.47746	0.	-0.25	5	0.2	1	-1
251	1	0.47746	0.	0.	5	0.2	1	-1
252	1	0.47746	0.	0.25	5	0.2	1	-1

Bonds # harmonic

1	1	1	2
2	1	1	22
3	1	1	232
4	1	2	3
5	1	2	23
6	1	2	233
7	1	3	4
8	1	3	24
9	1	3	234
10	1	4	5
11	1	4	25
12	1	4	235
13	1	5	6
14	1	5	26
15	1	5	236
16	1	6	7
17	1	6	27
18	1	6	237
19	1	7	8
20	1	7	28
21	1	7	238
22	1	8	9
23	1	8	29
24	1	8	239
25	1	9	10
26	1	9	30
27	1	9	240
28	1	10	11
29	1	10	31
30	1	10	241
31	1	11	12
32	1	11	32
33	1	11	242
34	1	12	13
35	1	12	33
36	1	12	243
37	1	13	14
38	1	13	34
39	1	13	244
40	1	14	15
41	1	14	35
42	1	14	245
43	1	15	16
44	1	15	36
45	1	15	246
46	1	16	17
47	1	16	37
48	1	16	247
49	1	17	18
50	1	17	38
51	1	17	248
52	1	18	19
53	1	18	39
54	1	18	249
55	1	19	20
56	1	19	40
57	1	19	250
58	1	20	21
59	1	20	41
60	1	20	251
61	1	21	42
62	1	21	252
63	1	22	23
64	1	22	43
65	1	23	24
66	1	23	44
67	1	24	25
68	1	24	45
69	1	25	26
70	1	25	46
71	1	26	27
72	1	26	47
73	1	27	28
74	1	27	48
75	1	28	29
76	1	28	49
77	1	29	30
78	1	29	50
79	1	30	31
80	1	30	51
81	1	31	32
82	1	31	52
83	1	32	33
84	1	32	53
85	1	33	34
86	1	33	54
87	1	34	35
88	1	34	55
89	1	35	36
90	1	35	56
91	1	36	37
92	1	36	57
93	1	37	38
94	1	37	58
95	1	38	39
96	1	38	59
97	1	39	40
98	1	39	60
99	1	40	41
100	1	40	61
101	1	41	42
102	1	41	62
103	1	42	63
104	1	43	44
105	1	43	64
106	1	44	45
107	1	44	65
108	1	45	46
109	1	45	66
110	1	46	47
111	1	46	67
112	1	47	48
113	1	47	68
114	1	48	49
115	1	48	69
116	1	49	50
117	1	49	70
118	1	50	51
119	1	50	71
120	1	51	52
121	1	51	72
122	1	52	53
123	1	52	73
124	1	53	54
125	1	53	74
126	1	54	55
127	1	54	75
128	1	55	56
129	1	55	76
130	1	56	57
131	1	56	77
132	1	57	58
133	1	57	78
134	1	58	59
135	1	58	79
136	1	59	60
137	1	59	80
138	1	60	61
139	1	60	81
140	1	61	62
141	1	61	82
142	1	62	63
143	1	62	83
144	1	63	84
145	1	64	65
146	1	64	85
147	1	65	66
148	1	65	86
149	1	66	67
150	1	66	87
151	1	67	68
152	1	67	88
153	1	68	69
154	1	68	89
155	1	69	70
156	1	69	90
157	1	70	71
158	1	70	91
159	1	71	72
160	1	71	92
161	1	72	73
162	1	72	93
163	1	73	74
164	1	73	94
165	1	74	75
166	1	74	95
167	1	75	76
168	1	75	96
169	1	76	77
170	1	76	97
171	1	77	78
172	1	77	98
173	1	78	79
174	1	78	99
175	1	79	80
176	1	79	100
177	1	80	81
178	1	80	101
179	1	81	82
180	1	81	102
181	1	82	83
182	1	82	103
183	1	83	84
184	1	83	104
185	1	84	105
186	1	85	86
187	1	85	106
188	1	86	87
189	1	86	107
190	1	87	88
191	1	87	108
192	1	88	89
193	1	88	109
194	1	89	90
195	1	89	110
196	1	90	91
197	1	90	111
198	1	91	92
199	1	91	112
200	1	92	93
201	1	92	113
202	1	93	94
203	1	93	114
204	1	94	95
205	1	94	115
206	1	95	96
207	1	95	116
208	1	96	97
209	1	96	117
210	1	97	98
211	1	97	118
212	1	98	99
213	1	98	119
214	1	99	100
215	1	99	120
216	1	100	101
217	1	100	121
218	1	101	102
219	1	101	122
220	1	102	103
221	1	102	123
222	1	103	104
223	1	103	124
224	1	104	105
225	1	104	125
226	1	105	126
227	1	106	107
228	1	106	127
229	1	107	108
230	1	107	128
231	1	108	109
232	1	108	129
233	1	109	110
234	1	109	130
235	1	110	111
236	1	110	131
237	1	111	112
238	1	111	132
239	1	112	113
240	1	112	133
241	1	113	114
242	1	113	134
243	1	114	115
244	1	114	135
245	1	115	116
246	1	115	136
247	1	116	117
248	1	116	137
249	1	117	118
250	1	117	138
251	1	118	119
252	1	118	139
253	1	119	120
254	1	119	140
255	1	120	121
256	1	120	141
257	1	121	122
258	1	121	142
259	1	122	123
260	1	122	143
261	1	123	124
262	1	123	144
263	1	124	125
264	1	124	145
265	1	125	126
266	1	125	146
267	1	126	147
268	1	127	128
269	1	127	148
270	1	128	129
271	1	128	149
272	1	129	130
273	1	129	150
274	1	130	131
275	1	130	151
276	1	131	132
277	1	131	152
278	1	132	133
279	1	132	153
280	1	133	134
281	1	133	154
282	1	134	135
283	1	134	155
284	1	135	136
285	1	135	156
286	1	136	137
287	1	136	157
288	1	137	138
289	1	137	158
290	1	138	139
291	1	138	159
292	1	139	140
293	1	139	160
294	1	140	141
295	1	140	161
296	1	141	142
297	1	141	162
298	1	142	143
299	1	142	163
300	1	143	144
301	1	143	164
302	1	144	145
303	1	144	165
304	1	145	146
305	1	145	166
306	1	146	147
307	1	146	167
308	1	147	168
309	1	148	149
310	1	148	169
311	1	149	150
312	1	149	170
313	1	150	151
314	1	150	171
315	1	151	152
316	1	151	172
317	1	152	153
318	1	152	173
319	1	153	154
320	1	153	174
321	1	154	155
322	1	154	175
323	1	155	156
324	1	155	176
325	1	156	157
326	1	156	177
327	1	157	158
328	1	157	178
329	1	158	159
330	1	158	179
331	1	159	160
332	1	159	180
333	1	160	161
334	1	160	181
335	1	161	162
336	1	161	182
337	1	162	163
338	1	162	183
339	1	163	164
340	1	163	184
341	1	164	165
342	1	164	185
343	1	165	166
344	1	165	186
345	1	166	167
346	1	166	187
347	1	167	168
348	1	167	188
349	1	168	189
350	1	169	170
351	1	169	190
352	1	170	171
353	1	170	191
354	1	171	172
355	1	171	192
356	1	172	173
357	1	172	193
358	1	173	174
359	1	173	194
360	1	174	175
361	1	174	195
362	1	175	176
363	1	175	196
364	1	176	177
365	1	176	197
366	1	177	178
367	1	177	198
368	1	178	179
369	1	178	199
370	1	179	180
371	1	179	200
372	1	180	181
373	1	180	201
374	1	181	182
375	1	181	202
376	1	182	183
377	1	182	203
378	1	183	184
379	1	183	204
380	1	184	185
381	1	184	205
382	1	185	186
383	1	185	206
384	1	186	187
385	1	186	207
386	1	187	188
387	1	187	208
388	1	188	189
389	1	188	209
390	1	189	210
391	1	190	191
392	1	190	211
393	1	191	192
394	1	191	212
395	1	192	193
396	1	192	213
397	1	193	194
398	1	193	214
399	1	194	195
400	1	194	215
401	1	195	196
402	1	195	216
403	1	196	197
404	1	196	217
405	1	197	198
406	1	197	218
407	1	198	199
408	1	198	219
409	1	199	200
410	1	199	220
411	1	200	201
412	1	200	221
413	1	201	202
414	1	201	222
415	1	202	203
416	1	202	223
417	1	203	204
418	1	203	224
419	1	204	205
420	1	204	225
421	1	205	206
422	1	205	226
423	1	206	207
424	1	206	227
425	1	207	208
426	1	207	228
427	1	208	209
428	1	208	229
429	1	209	210
430	1	209	230
431	1	210	231
432	1	211	212
433	1	211	232
434	1	212	213
435	1	212	233
436	1	213	214
437	1	213	234
438	1	214	215
439	1	214	235
440	1	215	216
441	1	215	236
442	1	216	217
443	1	216	237
444	1	217	218
445	1	217	238
446	1	218	219
447	1	218	239
448	1	219	220
449	1	219	240
450	1	220	221
451	1	220	241
452	1	221	222
453	1	221	242
454	1	222	223
455	1	222	243
456	1	223	224
457	1	223	244
458	1	224	225
459	1	224	245
460	1	225	226
461	1	225	246
462	1	226	227
463	1	226	247
464	1	227	228
465	1	227	248
466	1	228	229
467	1	228	249
468	1	229	230
469	1	229	250
470	1	230	231
471	1	230	251
472	1	231	252
473	1	232	233
474	1	233	234
475	1	234	235
476	1	235	236
477	1	236	237
478	1	237	238
479	1	238	239
480	1	239	240
481	1	240	241
482	1	241	242
483	1	242	243
484	1	243	244
485	1	244	245
486	1	245	246
487	1	246	247
488	1	247	248
489	1	248	249
490	1	249	250
491	1	250	251
492	1	251	252

Angles

1	1	2	1	22
2	1	2	1	232
3	1	1	2	23
4	1	1	2	233
5	1	3	2	23
6	1	3	2	233
7	1	2	3	24
8	1	2	3	234
9	1	4	3	24
10	1	4	3	234
11	1	3	4	25
12	1	3	4	235
13	1	5	4	25
14	1	5	4	235
15	1	4	5	26
16	1	4	5	236
17	1	6	5	26
18	1	6	5	236
19	1	5	6	27
20	1	5	6	237
21	1	7	6	27
22	1	7	6	237
23	1	6	7	28
24	1	6	7	238
25	1	8	7	28
26	1	8	7	238
27	1	7	8	29
28	1	7	8	239
29	1	9	8	29
30	1	9	8	239
31	1	8	9	30
32	1	8	9	240
33	1	10	9	30
34	1	10	9	240
35	1	9	10	31
36	1	9	10	241
37	1	11	10	31
38	1	11	10	241
39	1	10	11	32
40	1	10	11	242
41	1	12	11	32
42	1	12	11	242
43	1	11	12	33
44	1	11	12	243
45	1	13	12	33
46	1	13	12	243
47	1	12	13	34
48	1	12	13	244
49	1	14	13	34
50	1	14	13	244
51	1	13	14	35
52	1	13	14	245
53	1	15	14	35
54	1	15	14	245
55	1	14	15	36
56	1	14	15	246
57	1	16	15	36
58	1	16	15	246
59	1	15	16	37
60	1	15	16	247
61	1	17	16	37
62	1	17	16	247
63	1	16	17	38
64	1	16	17	248
65	1	18	17	38
66	1	18	17	248
67	1	17	18	39
68	1	17	18	249
69	1	19	18	39
70	1	19	18	249
71	1	18	19	40
72	1	18	19	250
73	1	20	19	40
74	1	20	19	250
75	1	19	20	41
76	1	19	20	251
77	1	21	20	41
78	1	21	20	251
79	1	20	21	42
80	1	20	21	252
81	1	1	22	23
82	1	23	22	43
83	1	2	23	22
84	1	2	23	24
85	1	22	23	44
86	1	24	23	44
87	1	3	24	23
88	1	3	24	25
89	1	23	24	45
90	1	25	24	45
91	1	4	25	24
92	1	4	25	26
93	1	24	25	46
94	1	26	25	46
95	1	5	26	25
96	1	5	26	27
97	1	25	26	47
98	1	27	26	47
99	1	6	27	26
100	1	6	27	28
101	1	26	27	48
102	1	28	27	48
103	1	7	28	27
104	1	7	28	29
105	1	27	28	49
106	1	29	28	49
107	1	8	29	28
108	1	8	29	30
109	1	28	29	50
110	1	30	29	50
111	1	9	30	29
112	1	9	30	31
113	1	29	30	51
114	1	31	30	51
115	1	10	31	30
116	1	10	31	32
117	1	30	31	52
118	1	32	31	52
119	1	11	32	31
120	1	11	32	33
121	1	31	32	53
122	1	33	32	53
123	1	12	33	32
124	1	12	33	34
125	1	32	33	54
126	1	34	33	54
127	1	13	34	33
128	1	13	34	35
129	1	33	34	55
130	1	35	34	55
131	1	14	35	34
132	1	14	35	36
133	1	34	35	56
134	1	36	35	56
135	1	15	36	35
136	1	15	36	37
137	1	35	36	57
138	1	37	36	57
139	1	16	37	36
140	1	16	37	38
141	1	36	37	58
142	1	38	37	58
143	1	17	38	37
144	1	17	38	39
145	1	37	38	59
146	1	39	38	59
147	1	18	39	38
148	1	18	39	40
149	1	38	39	60
150	1	40	39	60
151	1	19	40	39
152	1	19	40	41
153	1	39	40	61
154	1	41	40	61
155	1	20	41	40
156	1	20	41	42
157	1	40	41	62
158	1	42	41	62
159	1	21	42	41
160	1	41	42	63
161	1	22	43	44
162	1	44	43	64
163	1	23	44	43
164	1	23	44	45
165	1	43	44	65
166	1	45	44	65
167	1	24	45	44
168	1	24	45	46
169	1	44	45	66
170	1	46	45	66
171	1	25	46	45
172	1	25	46	47
173	1	45	46	67
174	1	47	46	67
175	1	26	47	46
176	1	26	47	48
177	1	46	47	68
178	1	48	47	68
179	1	27	48	47
180	1	27	48	49
181	1	47	48	69
182	1	49	48	69
183	1	28	49	48
184	1	28	49	50
185	1	48	49	70
186	1	50	49	70
187	1	29	50	49
188	1	29	50	51
189	1	49	50	71
190	1	51	50	71
191	1	30	51	50
192	1	30	51	52
193	1	50	51	72
194	1	52	51	72
195	1	31	52	51
196	1	31	52	53
197	1	51	52	73
198	1	53	52	73
199	1	32	53	52
200	1	32	53	54
201	1	52	53	74
202	1	54	53	74
203	1	33	54	53
204	1	33	54	55
205	1	53	54	75
206	1	55	54	75
207	1	34	55	54
208	1	34	55	56
209	1	54	55	76
210	1	56	55	76
211	1	35	56	55
212	1	35	56	57
213	1	55	56	77
214	1	57	56	77
215	1	36	57	56
216	1	36	57	58
217	1	56	57	78
218	1	58	57	78
219	1	37	58	57
220	1	37	58	59
221	1	57	58	79
222	1	59	58	79
223	1	38	59	58
224	1	38	59	60
225	1	58	59	80
226	1	60	59	80
227	1	39	60	59
228	1	39	60	61
229	1	59	60	81
230	1	61	60	81
231	1	40	61	60
232	1	40	61	62
233	1	60	61	82
234	1	62	61	82
235	1	41	62	61
236	1	41	62	63
237	1	61	62	83
238	1	63	62	83
239	1	42	63	62
240	1	62	63	84
241	1	43	64	65
242	1	65	64	85
243	1	44	65	64
244	1	44	65	66
245	1	64	65	86
246	1	66	65	86
247	1	45	66	65
248	1	45	66	67
249	1	65	66	87
250	1	67	66	87
251	1	46	67	66
252	1	46	67	68
253	1	66	67	88
254	1	68	67	88
255	1	47	68	67
256	1	47	68	69
257	1	67	68	89
258	1	69	68	89
259	1	48	69	68
260	1	48	69	70
261	1	68	69	90
262	1	70	69	90
263	1	49	70	69
264	1	49	70	71
265	1	69	70	91
266	1	71	70	91
267	1	50	71	70
268	1	50	71	72
269	1	70	71	92
270	1	72	71	92
271	1	51	72	71
272	1	51	72	73
273	1	71	72	93
274	1	73	72	93
275	1	52	73	72
276	1	52	73	74
277	1	72	73	94
278	1	74	73	94
279	1	53	74	73
280	1	53	74	75
281	1	73	74	95
282	1	75	74	95
283	1	54	75	74
284	1	54	75	76
285	1	74	75	96
286	1	76	75	96
287	1	55	76	75
288	1	55	76	77
289	1	75	76	97
290	1	77	76	97
291	1	56	77	76
292	1	56	77	78
293	1	76	77	98
294	1	78	77	98
295	1	57	78	77
296	1	57	78	79
297	1	77	78	99
298	1	79	78	99
299	1	58	79	78
300	1	58	79	80
301	1	78	79	100
302	1	80	79	100
303	1	59	80	79
304	1	59	80	81
305	1	79	80	101
306	1	81	80	101
307	1	60	81	80
308	1	60	81	82
309	1	80	81	102
310	1	82	81	102
311	1	61	82	81
312	1	61	82	83
313	1	81	82	103
314	1	83	82	103
315	1	62	83	82
316	1	62	83	84
317	1	82	83	104
318	1	84	83	104
319	1	63	84	83
320	1	83	84	105
321	1	64	85	86
322	1	86	85	106
323	1	65	86	85
324	1	65	86	87
325	1	85	86	107
326	1	87	86	107
327	1	66	87	86
328	1	66	87	88
329	1	86	87	108
330	1	88	87	108
331	1	67	88	87
332	1	67	88	89
333	1	87	88	109
334	1	89	88	109
335	1	68	89	88
336	1	68	89	90
337	1	88	89	110
338	1	90	89	110
339	1	69	90	89
340	1	69	90	91
341	1	89	90	111
342	1	91	90	111
343	1	70	91	90
344	1	70	91	92
345	1	90	91	112
346	1	92	91	112
347	1	71	92	91
348	1	71	92	93
349	1	91	92	113
350	1	93	92	113
351	1	72	93	92
352	1	72	93	94
353	1	92	93	114
354	1	94	93	114
355	1	73	94	93
356	1	73	94	95
357	1	93	94	115
358	1	95	94	115
359	1	74	95	94
360	1	74	95	96
361	1	94	95	116
362	1	96	95	116
363	1	75	96	95
364	1	75	96	97
365	1	95	96	117
366	1	97	96	117
367	1	76	97	96
368	1	76	97	98
369	1	96	97	118
370	1	98	97	118
371	1	77	98	97
372	1	77	98	99
373	1	97	98	119
374	1	99	98	119
375	1	78	99	98
376	1	78	99	100
377	1	98	99	120
378	1	100	99	120
379	1	79	100	99
380	1	79	100	101
381	1	99	100	121
382	1	101	100	121
383	1	80	101	100
384	1	80	101	102
385	1	100	101	122
386	1	102	101	122
387	1	81	102	101
388	1	81	102	103
389	1	101	102	123
390	1	103	102	123
391	1	82	103	102
392	1	82	103	104
393	1	102	103	124
394	1	104	103	124
395	1	83	104	103
396	1	83	104	105
397	1	103	104	125
398	1	105	104	125
399	1	84	105	104
400	1	104	105	126
401	1	85	106	107
402	1	107	106	127
403	1	86	107	106
404	1	86	107	108
405	1	106	107	128
406	1	108	107	128
407	1	87	108	107
408	1	87	108	109
409	1	107	108	129
410	1	109	108	129
411	1	88	109	108
412	1	88	109	110
413	1	108	109	130
414	1	110	109	130
415	1	89	110	109
416	1	89	110	111
417	1	109	110	131
418	1	111	110	131
419	1	90	111	110
420	1	90	111	112
421	1	110	111	132
422	1	112	111	132
423	1	91	112	111
424	1	91	112	113
425	1	111	112	133
426	1	113	112	133
427	1	92	113	112
428	1	92	113	114
429	1	112	113	134
430	1	114	113	134
431	1	93	114	113
432	1	93	114	115
433	1	113	114	135
434	1	115	114	135
435	1	94	115	114
436	1	94	115	116
437	1	114	115	136
438	1	116	115	136
439	1	95	116	115
440	1	95	116	117
441	1	115	116	137
442	1	117	116	137
443	1	96	117	116
444	1	96	117	118
445	1	116	117	138
446	1	118	117	138
447	1	97	118	117
448	1	97	118	119
449	1	117	118	139
450	1	119	118	139
451	1	98	119	118
452	1	98	119	120
453	1	118	119	140
454	1	120	119	140
455	1	99	120	119
456	1	99	120	121
457	1	119	120	141
458	1	121	120	141
459	1	100	121	120
460	1	100	121	122
461	1	120	121	142
462	1	122	121	142
463	1	101	122	121
464	1	101	122	123
465	1	121	122	143
466	1	123	122	143
467	1	102	123	122
468	1	102	123	124
469	1	122	123	144
470	1	124	123	144
471	1	103	124	123
472	1	103	124	125
473	1	123	124	145
474	1	125	124	145
475	1	104	125	124
476	1	104	125	126
477	1	124	125	146
478	1	126	125	146
479	1	105	126	125
480	1	125	126	147
481	1	106	127	128
482	1	128	127	148
483	1	107	128	127
484	1	107	128	129
485	1	127	128	149
486	1	129	128	149
487	1	108	129	128
488	1	108	129	130
489	1	128	129	150
490	1	130	129	150
491	1	109	130	129
492	1	109	130	131
493	1	129	130	151
494	1	131	130	151
495	1	110	131	130
496	1	110	131	132
497	1	130	131	152
498	1	132	131	152
499	1	111	132	131
500	1	111	132	133
501	1	131	132	153
502	1	133	132	153
503	1	112	133	132
504	1	112	133	134
505	1	132	133	154
506	1	134	133	154
507	1	113	134	133
508	1	113	134	135
509	1	133	134	155
510	1	135	134	155
511	1	114	135	134
512	1	114	135	136
513	1	134	135	156
514	1	136	135	156
515	1	115	136	135
516	1	115	136	137
517	1	135	136	157
518	1	137	136	157
519	1	116	137	136
520	1	116	137	138
521	1	136	137	158
522	1	138	137	158
523	1	117	138	137
524	1	117	138	139
525	1	137	138	159
526	1	139	138	159
527	1	118	139	138
528	1	118	139	140
529	1	138	139	160
530	1	140	139	160
531	1	119	140	139
532	1	119	140	141
533	1	139	140	161
534	1	141	140	161
535	1	120	141	140
536	1	120	141	142
537	1	140	141	162
538	1	142	141	162
539	1	121	142	141
540	1	121	142	143
541	1	141	142	163
542	1	143	142	163
543	1	122	143	142
544	1	122	143	144
545	1	142	143	164
546	1	144	143	164
547	1	123	144	143
548	1	123	144	145
549	1	143	144	165
550	1	145	144	165
551	1	124	145	144
552	1	124	145	146
553	1	144	145	166
554	1	146	145	166
555	1	125	146	145
556	1	125	146	147
557	1	145	146	167
558	1	147	146	167
559	1	126	147	146
560	1	146	147	168
561	1	127	148	149
562	1	149	148	169
563	1	128	149	148
564	1	128	149	150
565	1	148	149	170
566	1	150	149	170
567	1	129	150	149
568	1	129	150	151
569	1	149	150	171
570	1	151	150	171
571	1	130	151	150
572	1	130	151	152
573	1	150	151	172
574	1	152	151	172
575	1	131	152	151
576	1	131	152	153
577	1	151	152	173
578	1	153	152	173
579	1	132	153	152
580	1	132	153	154
581	1	152	153	174
582	1	154	153	174
583	1	133	154	153
584	1	133	154	155
585	1	153	154	175
586	1	155	154	175
587	1	134	155	154
588	1	134	155	156
589	1	154	155	176
590	1	156	155	176
591	1	135	156	155
592	1	135	156	157
593	1	155	156	177
594	1	157	156	177
595	1	136	157	156
596	1	136	157	158
597	1	156	157	178
598	1	158	157	178
599	1	137	158	157
600	1	137	158	159
601	1	157	158	179
602	1	159	158	179
603	1	138	159	158
604	1	138	159	160
605	1	158	159	180
606	1	160	159	180
607	1	139	160	159
608	1	139	160	161
609	1	159	160	181
610	1	161	160	181
611	1	140	161	160
612	1	140	161	162
613	1	160	161	182
614	1	162	161	182
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14

There are too many problems here to list them all and try to correct them all. Some highlights:

  1. Your model for the CNT is not stable. When run by itself it “explodes” almost instantly.
    initialafter20steps

  2. Your density for your liquid is insanely high resulting in extremely high pressure and energy. For the default of 16000 liquid atoms you have an initial energy of over 70 \epsilon per atom and a reduced pressure of nearly 150.

  3. Your timestep is too large

  4. You are starting from random positions for the liquid, so those will produce overlaps that have to be removed. If you read the documentation for the delete_atoms command carefully, you will find that it is very simple and straightforward to delete only overlapping atoms from the liquid group and leave the CNT untouched. e.g. with

delete_atoms overlap 0.2 liquid liquid
delete_atoms overlap 0.2 liquid cnt
  1. You should be doing a minimization before starting MD to remove excess potential energy.

But ultimately, everything already breaks down because of your bogus CNT model and parameters. Your system will not even run with a much shorter timestep and no liquid.

This is not really fixable from the LAMMPS side, this is just bad input. As has been pointed out many times, teaching you how to plan an prepare a proper simulation is beyond the scope of this forum and a discussion you need to have with your adviser and/or tutor because that needs first and foremost a good understanding of the physics of your model and how to correctly build a suitable geometry and choose adequate parameters. There is no “magic” command in LAMMPS that can just “fix” these issues.

1 Like
15

Thank you so much, these all a huge help. Helped a lot and gave me a lot of understanding of what I need to look for and how to proceed. I agree a lot of it is physics problems and not lammps, but since I am in the learning process some times I am confused what the source may be. Again thank you so much for explaning all this.

16

Dear akohlmey,

I am starting from the first point you mentioned that the cnt itself is unstable. To investigate and fix the unstability of the CNT I wanted to reproduce what you have shown in the image you posted. So I tried two ways: first I got rid of the liquid and tried to run the program heating up half of the CNT and deducting the heat from the other half. I got the Non-numeric atom coords again unless I commented out the “fix mvv …” then I could run it but cnt remains stable.

units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes

atom_style hybrid edpd full
bond_style harmonic
angle_style harmonic

region edpd block -20 20 -20 20 -10 10 units box
pair_style edpd 1.58 9872598

read_data tube1.dat

set atom * edpd/temp 5.0
set atom * edpd/cv 0.2

#grouping

group cnt type 1

compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes

comm_modify vel yes

velocity all create 1.0 432982 loop local dist gaussian

#fix mvv all mvv/edpd 0.5
fix cnt all edpd/source cuboid -10 20 -10 20.0 -10 10.0 0.01
fix cnt all edpd/source cuboid -10 20 -10 20.0 10 10.0 -0.01

timestep 0.001
run 500
reset_timestep 0

compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile

dump 1 all atom 1000 cnt.lammpstrj
dump_modify 1 scale no

run 500

I also tried having the liquid but with very low numbers of atoms (almost nothing) and watch the cnt. again the same error . Could you please tell me how where you able to run the cnt by itself that resulted in the exploded cnt?

this is the version with low liquid atoms:

units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes

atom_style hybrid edpd full
bond_style harmonic
angle_style harmonic

region edpd block -20 20 -20 20 -10 10 units box
pair_style edpd 1.58 9872598

read_data tube1.dat

create_atoms 2 random 5 276438 NULL

set atom * edpd/temp 5.0
set atom * edpd/cv 0.2

#grouping

group cnt type 1
group liquid type 2

#delete overlapping atoms as the liquid atoms are created randomely

comm_modify vel yes

delete_atoms overlap 0.2 liquid liquid
delete_atoms overlap 0.2 liquid cnt

compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes

comm_modify vel yes

velocity all create 1.0 432982 loop local dist gaussian

#fix mvv all mvv/edpd 0.2
fix cnt all edpd/source cuboid -20 40 -20 40.0 -10 20.0 0.001
fix liquid all edpd/source cuboid -20 40 -20 40.0 -10 20.0 -0.001

timestep 0.001
run 500
reset_timestep 0

compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile

dump 1 all atom 1000 cnt2.lammpstrj

run 500

I know as you mentioned previously there are even more problems + physics problems that I need to figure out consulting my advisor, but I would appreciate it if you can tell me how you did run the cnt by itself that resulted in the exploded one, coud you please share the file you ran?

Thanks a lot.

17

I am sorry, but I have spent more time on this than I have available already. What you are asking me is to act as your adviser and that is beyond my interest and the scope of this forum.

I just commented out the “create_atoms command” so that there is no liquid and inserted a minimize command before the run. The “exploded” output you saw is after 20 steps of minimization.

I will close this topic now. This has gone as far as it should. You can - of course - ask new questions, but they should be about LAMMPS and they should be specific.