Computing the angle between planes

LAMMPS users,

Is there a way within LAMMPS to compute the angle between two planes? I have a monoclinic cell and thus beta does not equal 90 degrees. I am wanting to calculate how beta changes as the simulation progresses. Is this possible within the LAMMPS code?

Thanks,

Ben

Thermo style prints the values of alpha beta and gamma for a cell see: http://lammps.sandia.gov/doc/thermo_style.html

When I add cellbeta to my thermo_style command, I get “Invalid keyword in thermo_style custom command.”

thermo 100
thermo_style custom time temp pe vol v_a_lattice v_c_lattice c_q1 c_q2 pxx pyy pzz density, cellbeta
thermo_modify norm yes

Note that I am using lammps version 5 Sep 2014

Are you sure it is cellbeta that is not recognized or “density,” ?

Ray

2015年7月10日 下午1:37於 “Benjamin Cowen” <[email protected]…24…>寫道:

I think I realized this right as you sent the email. Thanks.

Why would the angle beta be constant throughout a simulation that is operated in an NPT ensemble? The volume is allowed to fluctuate, but the angle beta does not change for the whole simulation. Even with other FFs, the angle beta is the same for the same crystal structure. I would expect this initially, but surprised it would not change slightly under NPT ensemble.

Does anyone know why the beta angle is fixed and does not change with FF or in NPT ensemble?

This is for a monoclinic crystal, so alpha=gamma = 90 but beta is not 90

Why would the angle beta be constant throughout a simulation that is
operated in an NPT ensemble? The volume is allowed to fluctuate, but the
angle beta does not change for the whole simulation. Even with other FFs,
the angle beta is the same for the same crystal structure. I would expect
this initially, but surprised it would not change slightly under NPT
ensemble.

Does anyone know why the beta angle is fixed and does not change with FF or
in NPT ensemble?

have a closer look at your fix npt command.

axel.

My specific command or the doc page?

My specific command or the doc page?

of course, both.

Does this have to do with the scalexy, scalexz, and scaleyz values being set to yes by default so they are scaled to the box shape?

I am not sure how the box-shape is staying the same, as I can watch the lattice constants, density, and volume vary.
I wanted to compare the value of beta with exp. results, but this value of beta just seems to be the input beta essentially.

I wanted to try to:

scalexz value = no,

But I keep getting that this is an unknown command.

Just finding it hard to compare beta with exp. results when it does not change as the volume of the box changes.

Is the command above not correct to allow the angle to change?

Figured out why the command did not work, forgot to put it in npt command.

Does this have to do with the scalexy, scalexz, and scaleyz values being set
to yes by default so they are scaled to the box shape?

no.

I am not sure how the box-shape is staying the same, as I can watch the
lattice constants, density, and volume vary.

if i was the teacher that taught you geometry, i would be very sad right now.
very simple example: can you have triangles that have all three angles
the same, but still a different area?

I wanted to compare the value of beta with exp. results, but this value of
beta just seems to be the input beta essentially.

I wanted to try to:

scalexz value = no,

But I keep getting that this is an unknown command.

Just finding it hard to compare beta with exp. results when it does not
change as the volume of the box changes.

Is the command above not correct to allow the angle to change?

how on earth should i be able to discuss whether a command is correct,
when i don't even know what command you are using?

if you set up fix npt correctly for triclinic cells, it will change
all 6 degrees of freedom of the cell. if it doesn't, it is likely
because you didn't allow lammps to do it.

axel.

My mistake, I misunderstood you. I said the volume should change with npt and you said to check npt. I thought you were saying it was not changing. Of course the angles can be the same with larger area.

I am using this command:

fix 1 all npt temp 300 300 0.02 x 1.01325 1.01325 0.2 y 1.01325 1.01325 0.2 z 1.01325 1.01325 0.2

I also had previously invoked the change box all triclinic command.

I am not sure how I am not using these command correctly. I have seen many examples which uses the same methodology. What am I doing wrong?

Thanks for your help,

Ben

Should i invoke the xy, xz, and yz command and allow those to fluctuate like I did with x,y, and z?

re-read the manual for fix npt more carefully. you currently get
exactly what you are asking for.
don't let others guess for you,*know* it for yourself.

axel.

p.s.: perhaps you should take sunday evenings off?