Re: Stress calculation

From: Abhaysinh Gaikwad (ahgaikwa_at_aggies.ncat.edu)
Date: Sun Jan 28 2018 - 15:50:37 CST

Hello Dr. Giacomo,

Thaks for replying.

As you said, I looked in the output log file but the 9 components of
pressure tensor are recorded as zero. I am using NAMD 2.11 Please see the
following output.

olvars: Collective variables biases initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars:
----------------------------------------------------------------------
colvars: The restart output state file will be
"SiAu_NIL_1.restart.colvars.state".
colvars: The final output state file will be "SiAu_NIL_1.colvars.state".
colvars: Writing to colvar trajectory file "SiAu_NIL_1.colvars.traj".
Pe 0 hosts 0 local and 124 remote patches for pe 1
Pe 0 hosts 0 local and 56 remote patches for pe 2
Info: useSync: 0 useProxySync: 0
Info: Startup phase 10 took 0.860276 s, 279.086 MB of memory in use
Info: Startup phase 11 took 0.000260115 s, 279.086 MB of memory in use
Info: Startup phase 12 took 0.00705481 s, 280.734 MB of memory in use
Info: Finished startup at 1.65893 s, 280.867 MB of memory in use

TCL: Running for 200 steps
REASSIGNING VELOCITIES AT STEP 0 TO 0 KELVIN.
Pe 1 has 0 local and 284 remote patches and 0 local and 3006 remote
computes.
Pe 2 has 0 local and 280 remote patches and 0 local and 2978 remote
computes.
PRESSURE: 0 0 0 0 0 0 0 0 0 0
GPRESSURE: 0 0 0 0 0 0 0 0 0 0
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG

ENERGY: 0 0.0000 0.0000 0.0000
0.0000 0.0000 18903937.2084 0.0000
277661520.0000 0.0000 296565457.2084 0.0000
296565457.2084 296565674.2422 0.0000

OPENING EXTENDED SYSTEM TRAJECTORY FILE
REASSIGNING VELOCITIES AT STEP 1 TO 0 KELVIN.
REASSIGNING VELOCITIES AT STEP 2 TO 0 KELVIN.
REASSIGNING VELOCITIES AT STEP 3 TO 0 KELVIN.
REASSIGNING VELOCITIES AT STEP 4 TO 0 KELVIN.
REASSIGNING VELOCITIES AT STEP 5 TO 0 KELVIN.
REASSIGNING VELOCITIES AT STEP 6 TO 0 KELVIN.
REASSIGNING VELOCITIES AT STEP 7 TO 0 KELVIN.
REASSIGNING VELOCITIES AT STEP 8 TO 0 KELVIN.
REASSIGNING VELOCITIES AT STEP 9 TO 0 KELVIN.
LDB: ============= START OF LOAD BALANCING ============== 3.79297
LDB: ============== END OF LOAD BALANCING =============== 3.79307
Info: useSync: 0 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 3.79505
REASSIGNING VELOCITIES AT STEP 10 TO 0 KELVIN.
REASSIGNING VELOCITIES AT STEP 11 TO 0 KELVIN.
REASSIGNING VELOCITIES AT STEP 12 TO 0 KELVIN.
REASSIGNING VELOCITIES AT STEP 13 TO 0 KELVIN.
REASSIGNING VELOCITIES AT STEP 14 TO 0 KELVIN.
REASSIGNING VELOCITIES AT STEP 15 TO 0 KELVIN.

I tried using pressure profile code available online to get the pressure
tensor values. Following is the code.

pressureProfile on
pressureProfileSlabs
pressureProfileFreq

I got an error that this is not supported in cuda version. In windows I
tried it the above code worked but the 9 components of pressure tensor were
still zero.
Could you please tell me if there any other code to get the pressure and
stress tensor components? I am using Lenard-Jones potential and CHARM++.

On Wed, Jan 17, 2018 at 11:42 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Hi Abhay, the 9 components of the pressure tensor will be printed to the
> standard output over time with the prefix "PRESSURE:", its running average
> with the prefix "PRESSAVG:", etc.
>
> I'm not sure what kind of potential energy you are using for such system:
> make sure that the force field you are using is appropriate by checking the
> literature.
>
> Giacomo
>
> On Tue, Jan 16, 2018 at 10:03 AM, Abhaysinh Gaikwad <
> ahgaikwa_at_aggies.ncat.edu> wrote:
>
>> Hello all,
>>
>> My system has two objects/geometries, one of silicon and one of gold. The
>> silicon is pushed on to the Gold to get a deformation in Gold. I am trying
>> to get the stress after the deformation of Gold. Please let me know if
>> there are any scripts available to calculate the stress generated after the
>> process?
>>
>>
>> Regards,
>> Abhay
>>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>

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