Ase interface #77

YuuuXie · 2019-09-27T13:59:37Z

add ase folder, and remove ase*.py in flare folder
ase module includes flare calculator, otf engine and logger
different md engines are tested with otf (src: otf_md.py, unit test: test_ase_setup/test_ase_otf.py with QE)
add .rst for mgp and ase in docs folder
cleaned up *.out in tests folder since they are not used

…interface

jonpvandermause · 2019-09-27T14:09:01Z

flare/ase/calculator.py

+        res.append(predict_on_atom((structure, atom, gp_model)))
+    return res
+
+def predict_on_structure_en(strucutre, gp_model):


Input should be "structure"

jonpvandermause · 2019-09-27T14:09:50Z

flare/ase/calculator.py

+
+        self.mgp_model = MappedGaussianProcess(self.gp_model, grid_params, struc_params)
+
+def predict_on_atom(params):


These functions look pretty similar to the ones in predict.py, would it be possible to use those so that we don't repeat code?

Good idea. I'll make the change

jonpvandermause · 2019-09-27T14:17:25Z

flare/mgp/otf.py

@@ -18,7 +17,7 @@
    qe_input_to_structure, parse_qe_forces
 from flare import output

-class MFFOTF(OTF):
+class MGPOTF(OTF):


We now have three otf.py files in the repo -- mgp/otf, which inherits from flare/otf, and ase/otf, which is separate. If there are common methods to all three, we should try to import them from one place to minimize duplication.

YuuuXie · 2019-09-27T14:25:02Z

Jon: We now have three otf.py files in the repo -- mgp/otf, which inherits from flare/otf, and ase/otf, which is separate. If there are common methods to all three, we should try to import them from one place to minimize duplication.

YuuuXie · 2019-09-27T14:29:25Z

One common method that can be extracted out is is_std_in_bound which is sort of independent. MGPOTF is short because it inherits most of the methods from OTF. ase/otf is coupled with ase calculator, ase logger and ase md engines, so will be harder to be put out

jonpvandermause · 2019-09-27T14:34:22Z

Yeah, is_std_in_bound would be good to have in one place (#30). We can either move it out of class in otf.py, or put it in predict.py.

YuuuXie · 2019-09-27T14:42:23Z

I can also have ase/otf to inherit from OTF somehow, since there're a lot of common attributes. Could we probably put is_std_in_bound in util.py? I think moving it in predict.py is a bit weird

YuuuXie

Oh I used to use the same dir as you do (../test_files/pseudos) and never passed TRAVIS test. Then Lixin figured out TRAVIS did its unit test in the tests folder, so it runs python test_ase_setup/test_ase_otf.py. That's why I changed it to test_files/pseudos and then it passed unit test

YuuuXie · 2019-09-27T14:15:54Z

flare/ase/calculator.py

+
+        self.mgp_model = MappedGaussianProcess(self.gp_model, grid_params, struc_params)
+
+def predict_on_atom(params):


Good idea. I'll make the change

jonpvandermause · 2019-09-28T13:47:25Z

Oh I used to use the same dir as you do (../test_files/pseudos) and never passed TRAVIS test. Then Lixin figured out TRAVIS did its unit test in the tests folder, so it runs python test_ase_setup/test_ase_otf.py. That's why I changed it to test_files/pseudos and then it passed unit test

Good catch. The test failed on my machine, but that's because I was running a different command than Travis. I switched it back.

codecov-io · 2019-09-28T15:00:58Z

Codecov Report

Merging #77 into master will increase coverage by 10.77%.
The diff coverage is 82.65%.

@@             Coverage Diff             @@
##           master      #77       +/-   ##
===========================================
+ Coverage   41.19%   51.97%   +10.77%     
===========================================
  Files          29       29               
  Lines        4954     4839      -115     
===========================================
+ Hits         2041     2515      +474     
+ Misses       2913     2324      -589

Impacted Files	Coverage Δ
flare/mgp/otf.py	`0% <0%> (ø)`	⬆️
flare/mgp/cubic_splines_numba.py	`5.87% <100%> (ø)`	⬆️
flare/mgp/splines_methods.py	`62.23% <100%> (+12.58%)`	⬆️
flare/struc.py	`97.16% <100%> (+0.16%)`	⬆️
flare/mgp/mgp.py	`98.17% <100%> (+2.76%)`	⬆️
flare/otf.py	`95.12% <100%> (+1.37%)`	⬆️
flare/ase/logger.py	`73.28% <73.28%> (ø)`
flare/ase/otf.py	`73.68% <73.68%> (ø)`
flare/ase/calculator.py	`92.85% <92.85%> (ø)`
flare/util.py	`91.11% <93.33%> (+1.11%)`	⬆️
... and 14 more

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anjohan · 2019-09-29T17:56:47Z

Re: Travis testing directory.

I set Travis to run its tests from the tests directory. When I try to run pytest from the base directory, I get a lot of errors from trying to locate ./test_files/cp2k_input_1.in etc.

…to ase_interface

YuuuXie · 2019-09-29T20:33:48Z

Re: Travis testing directory.

I set Travis to run its tests from the tests directory. When I try to run pytest from the base directory, I get a lot of errors from trying to locate ./test_files/cp2k_input_1.in etc.

I also tried running pytest ./ in the tests/ folder, but it works

YuuuXie · 2019-09-29T20:37:14Z

Yeah, is_std_in_bound would be good to have in one place (#30). We can either move it out of class in otf.py, or put it in predict.py.

The latest commits removed the predict functions in ase/otf.py, and uses predict.py. Also removed is_std_in_bound in otf.py and ase/otf.py, and moved it to util.py

This pull request can close #26 , #30 , #55

…interface

YuuuXie added 16 commits September 20, 2019 22:54

add ase

b2f8ee4

Merge branch 'master' of https://github.com/mir-group/flare into ase_…

a9148c3

…interface

ase otf passed unit test without parallel

856efe6

add struc <--> ase, close #26

6fb84ef

change ase module import

489ad8f

parallel calculator tested, use test_ase_otf.sh

83159a0

modify pseudo dir

336ea7d

add .rst for mgp and ase

7426a8d

4 ASE MD engines tested

1f57711

ase otf with mgp tested

fff9a87

pull from master

0c0b451

fix gp like

1909744

fix pseudo-pot path

a99da8d

clean test out files

66c5af0

delete redundant files

56e7f25

change test file

cc4b660

jonpvandermause reviewed Sep 27, 2019

View reviewed changes

add __init__ to flare/ase; correct pseudo dir

f4321be

YuuuXie commented Sep 28, 2019

View reviewed changes

jonpvandermause added 2 commits September 28, 2019 09:47

remove .. from pseudo dir

7115c03

correct pseudo dir again

ab4190e

YuuuXie added 2 commits September 29, 2019 16:27

ase uses predict.py and move is_std_in_bound out

06a297f

Merge branch 'ase_interface' of https://github.com/mir-group/flare in…

6cc9116

…to ase_interface

remove is_std_in_bound

36746d7

YuuuXie and others added 12 commits September 29, 2019 17:24

add ase tutorial

0ee0ab0

delete .swp

a2d8448

clean logger

fc047d2

Merge branch 'master' of https://github.com/mir-group/flare into ase_…

4039561

…interface

add output .xyz format

f7a5af1

add output .xyz format

7bcbed5

add doc for MGP and ASE

e0cf4bf

test mgp

1c890dd

modify docstrings

354739a

move global variables

01d767a

resolve global variable in cubic_spline_numba

00ff331

move global variables to filter_coeff

5a7da10

nw13slx merged commit 5523243 into master Oct 12, 2019

This was referenced Oct 12, 2019

is_std_in_bound() method from OTF could be moved to a new file #30

Closed

ASE interface unit test #55

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Ase interface #77

Ase interface #77

YuuuXie commented Sep 27, 2019

jonpvandermause Sep 27, 2019

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YuuuXie Sep 27, 2019

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anjohan commented Sep 29, 2019

YuuuXie commented Sep 29, 2019

YuuuXie commented Sep 29, 2019


		self.mgp_model = MappedGaussianProcess(self.gp_model, grid_params, struc_params)

		def predict_on_atom(params):

Ase interface #77

Ase interface #77

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