Unable to open file "Data Atoms.template" for reading.

[luizpzidoi]

Hi! I hope you are doing well!

I'm trying to run moltemplate.sh but I always get the following message:
########################################################

WARNING: atom_style unspecified

--> "Data Atoms" column data has an unknown format

Assuming atom_style = "full"

########################################################

And this happens if I try to run moltemplate.sh both for some example of the code and for some system I created. At the end of execution the following message is displayed:
lttree_postprocess.py v0.6.2 2021-4-20

Error(lttree_postprocess.py): Unable to open file
"Data Atoms.template"
for reading. (Do your files lack a "Data Atoms" section?)
(To override this error, run moltemplate using the "-nocheck" argument.)

Thank you!

[hothello]

The first warning is to inform the user that the atom_style full structure is assumed in your Data Atoms section. To get rid of this warning, set the style explicitly with: moltemplate.sh -atomstyle full yourscript.lt.

For the second error, it is impossible to say what is wrong without you sharing your input files.

[luizpzidoi]

Hi @hothello. I hope you are doing well.

Thank you so much for reply.
The first warning was caused by "atomstyle" parameter.
Thus the second, the error was in the input file, in the coordinates of the atoms. In moltemplate, the atoms name will be diferent. This error was happening because, for example, all carbon atoms was "C" and the correct is "C1, C2, etc".

[JShake7227]

Hi all,

I'm experiencing the second error mentioned above. It is not working with my system. Can anyone point me in the right direction of where I'm going wrong that doesn't permit a Data Atoms to be written?

Code

import "oplsaa.lt"
PEEK inherits OPLSAA {
create_var {$mol} # Force all monomers to share the same molecule-ID

atom-id mol-id atom-type charge x y z

write('Data Atoms') {
$atom:c11 $mol @atom:90 0.0 -6.354 0.347 -0.027 #1_ester_benzene
$atom:c12 $mol @atom:90 0.0 -6.172 1.723 0.175
$atom:c13 $mol @atom:90 0.0-4.906 2.333 0.186
$atom:c14 $mol @atom:90 0.0 -3.739 1.588 -0.023
$atom:c15 $mol @atom:90 0.0 -3.888 0.231 -0.288
$atom:c16 $mol @atom:90 0.0 -5.166 -0.366 -0.26
$atom:h12 $mol @atom:91 0.0 -7.053 2.345 0.33
$atom:h13 $mol @atom:91 0.0 -4.86 3.405 0.33
$atom:h15 $mol @atom:91 0.0 -3.062 -0.415 -0.546
$atom:h16 $mol @atom:91 0.0 -5.249 -1.438 -0.44
$atom:o11 $mol @atom:119 0.0 -7.499 -0.208 -0.012
$atom:c21 $mol @atom:222 0.0 -2.441 2.335 0.009 #2_Ketone
$atom:o21 $mol @atom:223 0.0 -2.493 3.574 0.03
$atom:c31 $mol @atom:90 0.0 -0.737 0.463 0.43 	#3_ester_benzene"
$atom:c32 $mol @atom:90 0.0 -1.067 1.752 0.013
$atom:c33 $mol @atom:90 0.0 -0.004 2.593 -0.386
$atom:c34 $mol @atom:90 0.0 1.33 2.156 -0.413
$atom:c35 $mol @atom:90 0.0 1.652 0.877 0.006
$atom:c36 $mol @atom:90 0.0 0.6 0.033 0.404
$atom:h31 $mol @atom:91 0.0 -1.484 -0.23 0.807
$atom:h33 $mol @atom:91 0.0 -0.227 3.618 -0.688
$atom:h34 $mol @atom:91 0.0 2.07 2.848 -0.796
$atom:h36 $mol @atom:91 0.0 0.828 -0.994 0.699
$atom:o31 $mol @atom:119 0.0 2.87 0.259 0.01
$atom:c41 $mol @atom:90 0.0 4.106 0.841 0.017 #4_non_terminal_benzene
$atom:c42 $mol @atom:90 0.0 4.453 2.169 0.234
$atom:c43 $mol @atom:90 0.0 5.8 2.565 0.204
$atom:c44 $mol @atom:90 0.0 6.815 1.627 0.014
$atom:c45 $mol @atom:90 0.0 6.484 0.286 -0.148
$atom:c46 $mol @atom:90 0.0 5.14 -0.096 -0.154
$atom:h42 $mol @atom:91 0.0 3.721 2.932 0.453
$atom:h43 $mol @atom:91 0.0 6.064 3.611 0.345
$atom:h44 $mol @atom:91 0.0 7.859 1.934 0.009
$atom:h45 $mol @atom:91 0.0 7.265 -0.465 -0.267
$atom:h46 $mol @atom:91 0.0 4.892 -1.149 -0.278

}

Data Bond List

write('Data Bond List') {
$bond:c12  $atom:c11 $atom:c12 # 1_ester_benzene
$bond:c23  $atom:c12 $atom:c13
$bond:c34  $atom:c13 $atom:c14
$bond:c45  $atom:c14 $atom:c15
$bond:c56  $atom:c15 $atom:c16
$bond:c61  $atom:c16 $atom:c11
$bond:c11o11 $atom:c11 $atom:o11 
$bond:c2h1 $atom:c12 $atom:h12
$bond:c3h3 $atom:c13 $atom:h13
$bond:c5h5 $atom:c15 $atom:h15
$bond:c6h6 $atom:c16 $atom:h16	
$bond:c21o21 $atom:c21 $atom:o21 #2_Ketone
$bond:c3132  $atom:c31 $atom:c32 #3_ester_benzene
$bond:c3233  $atom:c32 $atom:c33
$bond:c3334  $atom:c33 $atom:c34
$bond:c3435  $atom:c34 $atom:c35
$bond:c3536  $atom:c35 $atom:c36
$bond:c3631  $atom:c36 $atom:c31
$bond:c31h31 $atom:c31 $atom:h31
$bond:c33h33 $atom:c33 $atom:h33
$bond:c34h34 $atom:c34 $atom:h34
$bond:c35o31 $atom:c35 $atom:o31
$bond:c36h36 $atom:c36 $atom:h36
$bond:c4142  $atom:c41 $atom:c42 #4_non_terminal_benzene Start C1 Cation
$bond:c4243  $atom:c42 $atom:c43
$bond:c4344  $atom:c43 $atom:c44
$bond:c4445  $atom:c44 $atom:c45
$bond:c4546  $atom:c45 $atom:c46
$bond:c4641  $atom:c46 $atom:c41
$bond:c42h42 $atom:c42 $atom:h42
$bond:c43h43 $atom:c43 $atom:h43
$bond:c45h45 $atom:c45 $atom:h45
$bond:c46h46 $atom:c46 $atom:h46
$bond:b1 $atom:c14 $atom:c21	#Monomer Bonds
$bond:b2 $atom:c21 $atom:c32
$bond:b3 $atom:o31 $atom:c41

}
} # PEEK

Thank you and much appreciated.

[hothello]

Hi @JShake7227,
What you have shared is the definition of a molecule called PEEK. I suspect you compiled this script with moltemplate, which of course ends with an error because there isn't any statement to create a data file, such as:

sample = new PEEK[5].move(5,0,0)

Please take a look at the LAMMPS manual, Section 8.6.4: Moltemplate Tutorial. You need to create a master file that imports the OPLS-AA force field file and the PEEK molecule definition file and contains all the relevant sections to create a valid input deck for LAMMPS.

[JShake7227]

Hi @hothello,

Thank you for the guidance! That was the crux of my issue.

[jewettaij]

Yes, once you have defined a molecule, you need to specify how many copies of the molecule you want (and, perhaps also where you want them to go). (Otherwise a "Data Atoms.template" file will not be created.) That's what the "new" command does. (By convention, the "new" command(s) normally goes in the "system.lt" file, but you can name this file anything you want.)

As Otello mentioned, section 8.4 of the moltemplate manual explains how to arrange molecules in a rectangular grid.

(Separate issue: If you don't want to arrange your molecules in a 3-D grid, you can try using PACKMOL and run moltemplate.sh with the -xyz command line argument. Also see section. 8.9.1 of the moltemplate manual, for an alternative strategy to mix arbitrary numbers of different molecules together that doesn't require PACKMOL.)

But I'd start with the introductory chapter (chapter 4). It's really short.

And thank you again, Otello!
(Very much appreciated!)

[2838573741]

I am just starting to learn moltemplate. i want to model a 4H-SiC. Here is the sic4H.lt file and system.lt file I wrote. After running the command “moltemplate.sh -atomstyle full system.lt”, I get the following error"lttree_postprocess.py v0.6.2 2021-4-20

Error(lttree_postprocess.py): Unable to open file
"Data Atoms.template"
for reading. (Do your files lack a "Data Atoms" section?)
(To override this error, run moltemplate using the "-nocheck" argument.)".
Can you point me to the problem?

SiC4H.lt

SiC4H.lt

Defines the 4H-SiC unit cell for Moltemplate

Crystal system: Hexagonal, space group P6₃mc

Unit cell: a = 3.073 Å, c = 10.053 Å

Stacking sequence: ABCB

Atoms: 4 Si, 4 C

SiC4H {

Atom types and coordinates (x, y, z in Angstroms)

Format: $atom:id $mol type charge x y z

write("Data Atoms") {
$atom:Si1 $mol:.. @atom:Si 0.000000 0.000000 0.000000 # Si1
$atom:Si2 $mol:.. @atom:Si 1.536500 0.888000 2.513250 # Si2
$atom:Si3 $mol:.. @atom:Si 0.000000 1.776000 5.026500 # Si3
$atom:Si4 $mol:.. @atom:Si 1.536500 0.888000 7.539750 # Si4
$atom:C1 $mol:.. @atom:C 0.000000 0.000000 1.256625 # C1
$atom:C2 $mol:.. @atom:C 1.536500 0.888000 3.769875 # C2
$atom:C3 $mol:.. @atom:C 0.000000 1.776000 6.283125 # C3
$atom:C4 $mol:.. @atom:C 1.536500 0.888000 8.796375 # C4
}
write_once("In Init") {
units metal
atom_style full # <- Requires each atom has a MolID and Charge.
# This is not necessary. (Why use "full"?
# The "full" atom style is useful if you want to
# mix the aluminum with other molecules later.
# Otherwise, just use "atom_style atomic", and
# and remove the 2nd and 4th columns above.)
pair_style tersoff
}
write_once("In Settings") {
pair_coeff * * SiC_Erhart-Albe.tersoff Si Si Si Si C C C C
}
write_once("Data Masses") {
@atom:Si 28.09
@atom:C 12.01
}

}

system.lt

system.lt

Defines the 4H-SiC supercell for Moltemplate

Imports the unit cell definition from SiC4H.lt

Creates a 5x5x2 supercell

import "SiC4H.lt"

Define unit cell dimensions (in Angstroms)

a = 3.073 Å, y-boundary = a * sin(60°), c = 10.053 Å

write_once("Data Boundary") {
0.0 3.073 xlo xhi
0.0 2.660 ylo yhi # 3.073 * sin(60°)
0.0 10.053 zlo zhi
}

Replicate unit cell to form a 5x5x2 supercell

create_box 5 5 2

[hothello]

Hello @2838573741,
Please next time you post an issue, take the time to quote your input files properly using appropriate markdown handles.

As the error clearly states, no atom is created in your system.lt file. If you examine carefully the many examples provided for Moltemplate, you will see that the compiled file (say, system.lt) always contains one or more of the following statement(s):

wat  = new SPCE [10].move(0.00, 0.00, 3.10342) 
                [10].move(0.00, 3.10342, 0.01) 
                [10].move(3.10342, 0.01, 0.01)

This command:

creates 10x10x10 copies of the SPCE water molecule and arranges them in a (rather dense) cubic lattice with spacing 3.10342 Angstroms.

In your system.lt file, there is no such command. Also, you throw a create_box 5 5 2 line that is not for Moltemplate to execute, but rather should be passed to LAMMPS in a write_once("In Run") { ... } statement.... Except that it is not a valid LAMMPS command either. Also, the way you use the Tersoff pair coefficients is totally bogus: the sample contains 2 types (@atom:Si and @atom:C), therefore the mapping of Tersoff elements to atom types is Si C.
You would be better off referring to the LAMMPS documentation instead of trying random commands.

Here is what I would do. The philosophy is that Moltemplate creates a data file containing the unit cell, passes it to LAMMPS via a read_data system.data statement (which creates the simulation box), and then asks LAMMPS to replicate it and to do something with it. Here are my modified input scripts for your sample.

SiC4H.lt

# Defines the 4H-SiC unit cell for Moltemplate
# Crystal system: Hexagonal, space group P6_3mc
# Unit cell: a = 3.073 A, c = 10.053 A
# Stacking sequence: ABCB
# Atoms: 4 Si, 4 C

SiC4H {

 # Define unit cell dimensions (in Angstroms)
 # a = 3.073 A, y-boundary = a * sin(60), c = 10.053 A

 write_once("Data Boundary") {
  0.0  3.073 xlo xhi
  0.0  2.660 ylo yhi
  0.0 10.053 zlo zhi
 }

 # Atom types and coordinates (x, y, z in Angstroms)
 # Format: $atom:id $mol type charge x y z
 write("Data Atoms") {
  $atom:Si1 $mol:. @atom:Si 0. 0.000000 0.000000 0.000000
  $atom:Si2 $mol:. @atom:Si 0. 1.536500 0.888000 2.513250
  $atom:Si3 $mol:. @atom:Si 0. 0.000000 1.776000 5.026500
  $atom:Si4 $mol:. @atom:Si 0. 1.536500 0.888000 7.539750
  $atom:C1  $mol:. @atom:C  0. 0.000000 0.000000 1.256625
  $atom:C2  $mol:. @atom:C  0. 1.536500 0.888000 3.769875
  $atom:C3  $mol:. @atom:C  0. 0.000000 1.776000 6.283125
  $atom:C4  $mol:. @atom:C  0. 1.536500 0.888000 8.796375
 }
 
 write_once("In Init") {
  units metal
  atom_style full
  pair_style tersoff
 }

 write_once("In Settings") {
  pair_coeff * * /home/otello/.local/share/lammps/potentials/SiC_Erhart-Albe.tersoff Si C
 }

 write_once("Data Masses") {
  @atom:Si 28.09
  @atom:C 12.01
 }
}

system.lt

# Imports the unit cell definition from SiC4H.lt
# and force field specifications.
import "SiC4H.lt"
sample = new SiC4H

# Define the LAMMPS simulation:
# Create a 5x5x2 supercell
write_once("In Run") {
 replicate 5 5 2
 fix NVT all nvt temp 300 300 \$(100*dt)
 run 5000
}

Compile with the command:

moltemplate.sh -atomstyle full system.lt

Run LAMMPS:

lmp -in run.in.EXAMPLE 

[2838573741]

Hello @hothello,
Thank you very much for your answer! What you said is very correct! I have a question, why is it that the system.data file that I generate after compiling, has only spherical atoms in Ovito and no chemical bonds visible?

[hothello]

I hope you understood all the issues with your initial setup. There are no chemical bonds in the data file because that's the topology specified in SiC4H.lt. As you chose to use the Tersoff pair potential, there are no bonds in your system; otherwise, exclusion rules will apply.

[2838573741]

I probably get it, thanks again for the answer!