Storing and setting image flags within loop in LAMMPS input script

Hello,

I am doing a set of MC moves within a loop. I need to store the image flags, make a displacement move, check it and then reset if I don’t accept the move.

I’ve discovered that the image flags are available to be used as atom style variables within fix store/state but not through the set command (like x,y,z).

So I’ve gotten it to work with

fix image0 all store/state 0 ix iy iz
variable ixa equal f_image0[v_a][1]
variable iya equal f_image0[v_a][2]
variable iza equal f_image0[v_a][3]

Then later I have to use a loop over all atoms to reset each atom separately if I need to.

label loop
variable a loop {atoms} if "{reset1} == 1" then "set atom a image {ixa} {iya} {iza}
next a
jump SELF loopa

However, it seems that looping over all atoms is much slower than resetting an atom style variable via (set atom *) …such as x,y,z, etc.

Is there another way to store and reset image flags faster than a loop over all atoms within a LAMMPS script?

Also is there a way to turn off all the “Setting atom values for …” output in the LAMMPS output from the set command?

Thanks in advance.

Josh

Hello,

I am doing a set of MC moves within a loop. I need to store the image
flags, make a displacement move, check it and then reset if I don't accept
the move.

I've discovered that the image flags are available to be used as atom
style variables within fix store/state but not through the set command
(like x,y,z).

So I've gotten it to work with

fix image0 all store/state 0 ix iy iz
variable ixa equal f_image0[v_a][1]
variable iya equal f_image0[v_a][2]
variable iza equal f_image0[v_a][3]

Then later I have to use a loop over all atoms to reset each atom
separately if I need to.

label loop
variable a loop \{atoms\} if "{reset1} == 1" then "set atom a image {ixa} \{iya\} {iza}
next a
jump SELF loopa

However, it seems that looping over all atoms is much slower than
resetting an atom style variable via (set atom *) ..such as x,y,z, etc.

Is there another way to store and reset image flags faster than a loop
over all atoms within a LAMMPS script?

​the following change to the set command source will enable support for
atom style variables for set image

diff --git a/src/set.cpp b/src/set.cpp
index 4ed07d4..b97a961 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -327,15 +327,18 @@ void Set::command(int narg, char **arg)
       ximageflag = yimageflag = zimageflag = 0;
       if (strcmp(arg[iarg+1],"NULL") != 0) {
         ximageflag = 1;
- ximage = force->inumeric(FLERR,arg[iarg+1]);
+ if (strstr(arg[iarg+1],"v_") == arg[iarg+1])
varparse(arg[iarg+1],1);
+ else ximage = force->inumeric(FLERR,arg[iarg+1]);
       }
       if (strcmp(arg[iarg+2],"NULL") != 0) {
         yimageflag = 1;
- yimage = force->inumeric(FLERR,arg[iarg+2]);
+ if (strstr(arg[iarg+2],"v_") == arg[iarg+2])
varparse(arg[iarg+2],2);
+ else yimage = force->inumeric(FLERR,arg[iarg+2]);
       }
       if (strcmp(arg[iarg+3],"NULL") != 0) {
         zimageflag = 1;
- zimage = force->inumeric(FLERR,arg[iarg+3]);
+ if (strstr(arg[iarg+3],"v_") == arg[iarg+3])
varparse(arg[iarg+3],3);
+ else zimage = force->inumeric(FLERR,arg[iarg+3]);
       }
       if (ximageflag && ximage && !domain->xperiodic)
         error->all(FLERR,
@@ -789,6 +792,9 @@ void Set::set(int keyword)
       int xbox = (atom->image[i] & IMGMASK) - IMGMAX;
       int ybox = (atom->image[i] >> IMGBITS & IMGMASK) - IMGMAX;
       int zbox = (atom->image[i] >> IMG2BITS) - IMGMAX;
+ if (varflag1) ximage = static_cast<int>(xvalue);
+ if (varflag2) yimage = static_cast<int>(yvalue);
+ if (varflag3) zimage = static_cast<int>(zvalue);
       if (ximageflag) xbox = ximage;
       if (yimageflag) ybox = yimage;
       if (zimageflag) zbox = zimage;

​...and here is a small demo input:​

region box block 0 1 0 1 0 1
atom_modify map array
create_box 1 box

pair_style zero 1.0
pair_coeff * *
mass * 1.0

create_atoms 1 single 0.25 0.25 0.5
create_atoms 1 single 0.75 0.25 0.5
create_atoms 1 single 0.25 0.5 0.5
create_atoms 1 single 0.5 0.5 0.5

variable cx equal xcm(all,x)
variable cy equal xcm(all,y)
variable cz equal xcm(all,z)

print "\{cx\} {cy} ${cz}"

fix 1 all store/state 0 ix iy iz

run 0 post no

set atom 1:2 image 1 1 -1

print "\{cx\} {cy} ${cz}"

variable imgx atom f_1[1]
variable imgy atom f_1[2]
variable imgz atom f_1[3]

set atom * image v_imgx v_imgy v_imgz

print "\{cx\} {cy} ${cz}"

​axel.​

Also is there a way to turn off all the "Setting atom values for ..."
output in the LAMMPS output from the set command?

​​

Excellent. Thank you!

Hi Axel,

This works well as far as I can tell. I didn’t see it in a pull request. Were you going to submit it or do you want me to do it and update the doc page?

Thanks.

Josh

Hi Axel,

This works well as far as I can tell. I didn't see it in a pull request.
Were you going to submit it or do you want me to do it and update the doc
page?

​all done. it is in my "meta pull request​", currently #510

for steve to not have 10s of pull requests with such small changes (one
line fixes, or local changes without side effects), i collect them into a
single PR. here is the commit.

​axel.​

Thanks. Sorry, I didn’t see it there.