Comments (9)
Hi Anne,
I think the syntax should be
pot.calc(a,energy=True)
It's difficult to say which subroutine is executed, because it depends on
the potential that you initialised. For example, for SW that will invoke a
chain like this:
potential_calc() in Potential.f95
Potential_Simple_Calc() in Potential_Simple.f95
IP_calc() in IP.f95
IPModel_SW_Calc() in IPModel_SW.f95
and that's the lowest level, apart from some auxiliary
routines IPModel_SW_Calc() might call.
I hope this helps.
Albert
On 23 August 2016 at 19:12, astronomydomine2 [email protected]
wrote:
Hello,
I am trying to understand how exactly the energy of a group of atoms is
calculated given an input of the atomic structure and the potential. From
what I understand, after the potential is defined (pot = Potential(...)),
this is executed as the pot.calc(a,'energy=energy') method (or something
similar).Would you be able to please point me to which exact file has this
subroutine with the actual lines that do this calculation at the lowest
level?Thanks,
Anne—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
#38, or mute the thread
https://github.com/notifications/unsubscribe-auth/AEKWQuGwhgdaDXC0BU7pwc4QPNts1lUhks5qizgVgaJpZM4JrOTa
.
Dr Albert Bartok-Partay
Leverhulme Early Career Fellow
Department of Engineering, University of Cambridge, Cambridge, CB21PZ
Magdalene College, Cambridge, CB30AG
T: +44 1223 748232
W: http://www.bartokpartay.com
E: [email protected]
PGP public key: http://pgp.mit.edu (ID:FC646FB1)
from quip.
Thanks a lot; is there any publication or documentation on how you got the exact formula to compute energy based on potential, for the different potentials?
Thanks
Anne
from quip.
Most are based on the appropriate publications - sometimes this is
documented in the code, but very often it is evident given the name of the
potential. Which ones are you interested in?
Albert
On 24 August 2016 at 14:44, astronomydomine2 [email protected]
wrote:
Thanks a lot; is there any publication or documentation on how you got the
exact formula to compute energy based on potential, for the different
potentials?Thanks
Anne—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
#38 (comment), or mute
the thread
https://github.com/notifications/unsubscribe-auth/AEKWQkuTBlS5IaXPk9BTxbS7Uv2Me6dxks5qjEqzgaJpZM4JrOTa
.
from quip.
Hi Albert,
I am interested in potentials for quartz and borosilicate glass.
From what I understand quartz uses: p = Potential('IP TS', param_filename='TS_params.xml')
Do you know what would be most appropriate for borosilicate glass?
I looked up the Yukawa potential/screened Coulomb potential but could not determine what sort of algorithm computes the energy. My goal is to get Ebulk and Eslab to calculate gamma (surface energy density)
Thanks
Anne
from quip.
The TS potential implemented in QUIP uses a short-range Coulomb interaction with the Yukawa method. The exact formulation as well as parameters for SiO2 (same as those in the .xml file you mention) are reported in this article:
http://scitation.aip.org/content/aip/journal/jcp/133/9/10.1063/1.3475565
It might be possible to use it for borosilicates too but would require reparameterisation.
from quip.
Thank you James. I looked through the equations in the paper; is it the Eqq+Eqd+Edd sum for every atom pair, as listed in equations 4-6? I am a bit unclear still on how energy computed.
I am looking at surface.py. It looks like after the input of surface atoms, bulk atoms, and potential, the surface.energy is computed using pot.calc(surface...) and bulk.energy is calculated using pot.calc(bulk...). I am interested in understanding how exactly these quantities are computed before being plugged into bulk_energy_per_sio2 and the final returned surface energy value.
def surface_energy(pot, bulk, surface, dir=2):
if not hasattr(bulk, 'energy'):
bulk.calc_connect()
pot.calc(bulk, energy=True, force=True)
bulk_energy_per_sio2 = bulk.energy/(bulk.z == 14).sum()
surface.calc_connect()
pot.calc(surface, energy=True, force=True)
area = surface.cell_volume()/surface.lattice[dir,dir]
return (surface.energy - (surface.z == 14).sum()*bulk_energy_per_sio2)/(2.0*area)
from quip.
Those equations give the electrostatic contribution to the potential energy. There is also a short-range Morse-Stretch term. You can find all the details in the Calc
interface in src/Potetials/IPModel_TS.f95
:
https://github.com/libAtoms/QUIP/blob/public/src/Potentials/IPModel_TS.f95#L417
from quip.
Can I close this now?
from quip.
from quip.
Related Issues (20)
- RMSE for Liquids in GAP HOT 6
- pip install quippy-ase error HOT 10
- OS/Python version combination (in connection to pip install quippy-ase error #623) HOT 20
- cpu overhead during potential file reading HOT 5
- Compilation Error HOT 5
- Error while reading old trained models and dimer descriptors issue HOT 5
- Regarding Absolute Error of configurations of training set
- fatal error: mach/host_info.h: No such file or directory HOT 4
- Compilation Error HOT 1
- General trimer descriptor and gap_fit HOT 5
- QUIPPY installation issue
- SYSTEM ABORT: Traceback (most recent call last) File "/io/QUIP/src/GAP/gp_predict.f95", line 485 kind unspecified HOT 7
- gap_fit MPI Segmentation fault HOT 20
- Let's have the makefiles cry with very old compiler versions HOT 1
- gap_si_surface.ipynb: runtime error about dftb-params.xml HOT 1
- angle_3b not MPI ready HOT 2
- Empty output file from quip command HOT 37
- SYSTEM ABORT: Database was created with a later version of the code. (in LAMMPS) HOT 2
- LAMMPS + QUIP HOT 1
- Why is it possible to use multiple descriptors in the gap_fit command? HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from quip.