Re: Stress calculation

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Jan 29 2018 - 10:17:58 CST

Hi Abhay, there are several puzzling things with your input. You have:
- defined a bias on a collective variable, which is probably going to
contribute to the virial stress in ways that you don't intend (see the huge
MISC energy)
- you have a system where the only energy term is the Lennard-Jones
potential and the total LJ energy is positive: what does that tell you?
- you're reassigning velocities to maintain a temperature of 0K.

Before dealing with technical issues (which I don't see signs of) you may
want to re-examine the physical model you have used. The first sensible
step would be to reproduce a similar result from the literature, and follow
the published protocol. For every line that you put in the configuration
file, you must understand its meaning: no copy-paste.

Lastly, you had posted the same question yesterday (which was not a working
day for most people) and just re-posted it again because you wanted a quick
reply. Considering that replies to the mailing list are volunteer work,
this was a bit rude on your part.

Giacomo

On Mon, Jan 29, 2018 at 11:04 AM, Abhaysinh Gaikwad <
ahgaikwa_at_aggies.ncat.edu> wrote:

> 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
>>
>
>
>

-- 
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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