PBC gaussian #706

anbenali · 2018-03-25T16:51:04Z

This is a fully working version with tests. I am still creating tests specially for Real Kpoints different than Gamma.

…elop

…Warning PyscfToQMCPACK broken

…c/QMCTools/PyscfToQmcpack.py .. I think

…ercells

…et PBC

…der for SPO. No implementation for H5 multidets; Decision is needed

…on. Need piping from XML

qmc-robot · 2018-03-25T16:53:01Z

Can one of the maintainers verify this patch?

qmc-robot · 2018-03-25T16:53:03Z

Can one of the maintainers verify this patch?

…ely read from XML input

…ut imagnary part is 0

Merge branch 'PBC-Gaussian' of https://github.com/anbenali/qmcpack into PBC-Gaussian

prckent · 2018-03-25T21:39:56Z

OK to test

prckent · 2018-03-25T22:02:18Z

Initial trivial comment about the files: can you use a link to C.BFD.xml instead of duplicating the file? Or is this file somehow different from the other C potentials we have used?

ye-luo · 2018-03-26T17:26:37Z

tests/solids/diamondC_1x1x1-Gaussian_pp/CMakeLists.txt

+  LIST(APPEND LONG_DIAMOND_SCALARS "totenergy" "-10.4951 0.0017")
+  LIST(APPEND LONG_DIAMOND_SCALARS "samples" "192640 0.0")
+
+# Reference VMC run in qmc-ref "-10.496089 0.000159"


Move this line before all the two lines of LIST and update the value

ye-luo · 2018-03-26T17:27:03Z

tests/solids/diamondC_1x1x1-Gaussian_pp/CMakeLists.txt

+
+
+# Reference DMC run in qmc-ref "-10.531770  0.000937"
+  LIST(APPEND LONG_DIAMOND_DMC_SCALARS "totenergy" "-10.544774 0.014408")


Put consistent value.

ye-luo · 2018-03-26T17:27:27Z

tests/solids/diamondC_2x1x1-Gaussian_pp/CMakeLists.txt

+                    )
+
+# Reference DMC run in qmc-ref "-21.845935 +/- 0.003098"
+  LIST(APPEND DIAMOND_DMC_SCALARS "totenergy" "-21.807657 0.095185")


Put consistent value

ye-luo · 2018-03-26T17:29:44Z

Found many inconsistency in CMakeLists.txt for tests.
The reference values need to be set based on the qmc_ref long and wide runs.
The reference error bar should be put based on the short/long runs.
The walkers in the input file should be set 16 and the samples need to computed accordingly.

jtkrogel · 2018-03-26T19:19:51Z

This is what I generally do for test creation:

Run one very long run (lots of steps and blocks) to generate reference data. This reduces both the error bar and the error bar of the error bar (10x longer than long test, 100x longer than short test).
Reproduce the very long run, but with fewer blocks to save as reference data (scalar.dat files) with the commit.
Use the reference error bar to appropriately estimate the error bar for the long and short tests. These error bars are sqrt(10+1) and sqrt(100+1) times larger than the very long reference.

prckent · 2018-03-27T02:14:17Z

@jtkrogel gives the appropriate procedure

ye-luo · 2018-03-28T17:55:03Z

I added a How to add tests wikipage to collect our requirements for tests. Let us update that one.

prckent · 2018-03-28T18:20:15Z

I currently plan to approve this after the tests are updated and the "Master list of required changes:" is then completed, probably this evening. If people have significant concerns that need to be addressed now (vs later updates) then comment soon.

anbenali · 2018-03-28T18:56:59Z

following @prckent comment, the tests are important but they are not needed to check the code.. so reviewers can/should let me know if something in the code seems fishy..

ye-luo

Just to prevent merging, I have doubts in the code.

ye-luo · 2018-03-29T02:19:15Z

src/QMCWaveFunctions/Fermion/SlaterDetBuilder.cpp

  //check the basis set
  cur = curRoot->children;
  while (cur != NULL)//check the basis set
  {
    getNodeName(cname,cur);
-    if (cname == basisset_tag)
+    if (cname == basisset_tag || H5ReadOnce==true )


@anbenali could you send me by email the case that the code will crash without this part of change.

ye-luo · 2018-03-29T02:27:08Z

src/QMCWaveFunctions/lcao/SoaLocalizedBasisSet.h

+  */
+  void setPBCImages(std::vector<int> PBCImages)
+  {
+    for(int c=0; c<NumCenters; c++)


Better to loop directly LOBasisSet.size(). Similar to the makeClone routine above.
Loop over NumCenters is redundant.

ye-luo · 2018-03-29T02:30:48Z

src/QMCWaveFunctions/lcao/SoaAtomicBasisSet.h

@@ -89,8 +90,14 @@ namespace qmcplusplus
      {
        return BasisSetSize;
      }//=NL.size(); 
+      // Set the number of periodic image for the evaluation of the orbitals. 
+      void setPBCImages(std::vector <int> PBCImages)


I don't like the naming inconsistency between PBCImages and MaxCell. Choose one.
std::vector is not a good type.
TinyVector<int,3> is better.

anbenali · 2018-03-29T02:32:57Z

It will not crash... tested it again. It was crashing for another reason that was debugged in the process.. if you call it inside (same way you tried it first) it will still work.

…

On Wed, Mar 28, 2018 at 9:19 PM, Ye Luo ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In src/QMCWaveFunctions/Fermion/SlaterDetBuilder.cpp <#706 (comment)>: > //check the basis set cur = curRoot->children; while (cur != NULL)//check the basis set { getNodeName(cname,cur); - if (cname == basisset_tag) + if (cname == basisset_tag || H5ReadOnce==true ) @anbenali <https://github.com/anbenali> could you send me by email the case that the code will crash without this part of change. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#706 (review)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AXl6w1SxnjkdDR_z0aViYCWZlOJv8beSks5tjESlgaJpZM4S6Niy> .

-- ----------------------- Anouar Benali, PhD Leadership Computing Facility Argonne National Laboratory Building 240 Office - 2127 9700 S Cass Av., Argonne Il, 60439 (630) 252-0058

anbenali · 2018-03-29T02:33:52Z

Can you put it in an example. I tried multiple approaches to reduce redundancies but was not successful.

…

On Wed, Mar 28, 2018 at 9:27 PM, Ye Luo ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In src/QMCWaveFunctions/lcao/SoaLocalizedBasisSet.h <#706 (comment)>: > @@ -88,8 +88,17 @@ struct SoaLocalizedBasisSet: public RealBasisSetBase<typename COT::value_type> myclone->LOBasisSet[i]=LOBasisSet[i]->makeClone(); return myclone; } + /** set Number of periodic Images to evaluate the orbitals. + Set to 0 for non-PBC, and set manually in the input. + */ + void setPBCImages(std::vector<int> PBCImages) + { + for(int c=0; c<NumCenters; c++) Better to loop directly LOBasisSet.size(). Loop over NumCenters is redundant. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#706 (review)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AXl6w6K3x5ILHPnJUdfMmI_0mvIcFmbCks5tjEZ9gaJpZM4S6Niy> .

-- ----------------------- Anouar Benali, PhD Leadership Computing Facility Argonne National Laboratory Building 240 Office - 2127 9700 S Cass Av., Argonne Il, 60439 (630) 252-0058

ye-luo · 2018-03-29T02:37:37Z

In this PR, some SPOSetBase routines are copied over to LCAOSetBuilder file and modified for PBC. This is "wrong" in principle. The reason for this situation is that these methods introduced for AoS should not be in the base class but in the builder. This will be fixed after this PR.

ye-luo · 2018-03-29T03:34:02Z

binpad can hold 64 states at maximum and 64 is hard-coded. Need to be replaced.

anbenali · 2018-03-29T04:01:01Z

binpad will be replaced in a subsequent PR as it only concerns the multideterminant storage in the converter. There is no read of it QMCPACK.

…

On Wed, Mar 28, 2018 at 10:34 PM, Ye Luo ***@***.***> wrote: binpad can hold 64 states at maximum and 64 is hard-coded. Need to be replaced. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#706 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AXl6wwGE7h0h3aFLE_s8pzCYmg-1HX2vks5tjFYqgaJpZM4S6Niy> .

-- ----------------------- Anouar Benali, PhD Leadership Computing Facility Argonne National Laboratory Building 240 Office - 2127 9700 S Cass Av., Argonne Il, 60439 (630) 252-0058

prckent · 2018-03-29T12:39:16Z

For "do later" items, please create GitHub issues as I have just done so that they are not "forgotten"

anbenali added 16 commits January 30, 2018 22:38

Merge branch 'develop' of https://github.com/QMCPACK/qmcpack into dev…

cc2db2d

…elop

Step 1: All piping Done + Periodic eval of Psi; Remaining: Gradiant! …

a9c445f

…Warning PyscfToQMCPACK broken

Workinggit add ../src/QMCWaveFunctions/lcao/SoaAtomicBasisSet.h ../sr…

ecd4280

…c/QMCTools/PyscfToQmcpack.py .. I think

Working and tested. Need sposet for multidets

f5bcdce

Tests from Molecular pyscf corrected! All good to go. Testing for sup…

0ae8873

…ercells

END OF PBC Gaussians. This is the split in the PR

d522994

Should probably be new PR : SPOSET SOA with HDF5 handling for Multid…

4c8d8b1

…et PBC

Step 2 in sposet. still debugging

7baf4ff

Working VMC/DMC for Multideterminants Gaussians with PBC - with H5rea…

234511e

…der for SPO. No implementation for H5 multidets; Decision is needed

Fixes for Spherical harmonics

81e44e2

Test case Carbon Diamond 1x1x1

f0f11cf

symlinks to reduce number of files

4bb8e22

Tests LDA Gaussian complete

d10bfd9

Forgotten file

30199e2

Adding endpoint implementation of NbImages to be used in the evaluati…

3d8a1e7

…on. Need piping from XML

Remove old commented implemnatation

903842d

anbenali requested review from ye-luo, jngkim and prckent March 25, 2018 16:51

ghost assigned anbenali Mar 25, 2018

ghost added the in progress label Mar 25, 2018

FULLY COMPLETED: Nb of Periodic images to evaluate orbitals effectiv…

0c34c3b

…ely read from XML input

anbenali changed the title ~~[WIP] Pbc gaussian~~ PBC gaussian Mar 25, 2018

anbenali added 3 commits March 25, 2018 14:50

Merge branch 'develop' into PBC-Gaussian

d4e8bc6

Forgotten to re-enable when kpoints are defined as Complex in pyscf b…

0e18560

…ut imagnary part is 0

I do not know why this is here

9eb35e5

Merge branch 'PBC-Gaussian' of https://github.com/anbenali/qmcpack into PBC-Gaussian

ye-luo reviewed Mar 26, 2018

View reviewed changes

Reference for diamond 1x1x1

f3878f8

ye-luo requested changes Mar 29, 2018

View reviewed changes

ye-luo reviewed Mar 29, 2018

View reviewed changes

anbenali added 3 commits March 28, 2018 23:08

All tests + minor fixes

e819f3a

Final Push. All requests answered

292bb3b

Merge branch 'develop' into PBC-Gaussian

a0e8aa3

ye-luo approved these changes Mar 29, 2018

View reviewed changes

This was referenced Mar 29, 2018

Add manual documentation of periodic Gaussians and PySCF support #720

Closed

Remove fixed size limits on binpad for Gaussian multideterminant conversion #721

Open

prckent approved these changes Mar 29, 2018

View reviewed changes

prckent merged commit 9465c5f into QMCPACK:develop Mar 29, 2018

ghost removed the in progress label Mar 29, 2018

anbenali deleted the PBC-Gaussian branch June 21, 2018 21:27

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PBC gaussian #706

PBC gaussian #706

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prckent commented Mar 29, 2018



		# Reference DMC run in qmc-ref "-10.531770 0.000937"
		LIST(APPEND LONG_DIAMOND_DMC_SCALARS "totenergy" "-10.544774 0.014408")

PBC gaussian #706

PBC gaussian #706

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