mlatom 2.1.3__tar.gz → 2.2.1__tar.gz

{MLatom-2.1.3 → MLatom-2.2.1}/PKG-INFO

@@ -1,12 +1,11 @@
 Metadata-Version: 2.1
 Name: MLatom
-Version: 2.1.3
+Version: 2.2.1
 Summary: A Package for Atomistic Simulations with Machine Learning
 Home-page: http://mlatom.com
 Author: Pavlo O. Dral
 Author-email: admin@mlatom.com
 License: CC BY-NC-ND 4.0
-Platform: UNKNOWN
 Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Fortran
@@ -127,7 +126,7 @@ MLatom also provides interfaces to some third-party software where extra ML mode
 
 # About Program
 MLatom: a Package for Atomistic Simulations with Machine Learning    
-Version 2.1.3
+Version 2.2.1
 http://mlatom.com/                             
                                                                            
 Copyright (c) 2013-2022 Pavlo O. Dral                   
@@ -141,7 +140,7 @@ Cite as:
 
 1. Pavlo O. Dral, J. Comput. Chem. 2019, 40, 2339-2347             
 2. Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr, Jianxing Huang, Mario Barbatti, Top. Curr. Chem. 2021, 379, 27              
-3. Pavlo O. Dral, Peikun Zheng, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr, MLatom: A Package for Atomistic Simulations with Machine Learning, version 2.1.3, Xiamen University, Xiamen, China, 2013-2022.               
+3. Pavlo O. Dral, Peikun Zheng, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr, MLatom: A Package for Atomistic Simulations with Machine Learning, version 2.2.1, Xiamen University, Xiamen, China, 2013-2022.               
 
 
 # License
@@ -149,5 +148,3 @@ Cite as:
 This work is licensed under the [Attribution-NonCommercial-NoDerivatives 4.0 International](http://creativecommons.org/licenses/by-nc-nd/4.0/) license. See LICENSE.CC-BY-NC-ND-4.0.
 
 <a rel="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-nd/4.0/88x31.png" /></a>
-
-

{MLatom-2.1.3 → MLatom-2.2.1}/README.md

@@ -109,7 +109,7 @@ MLatom also provides interfaces to some third-party software where extra ML mode
 
 # About Program
 MLatom: a Package for Atomistic Simulations with Machine Learning    
-Version 2.1.3
+Version 2.2.1
 http://mlatom.com/                             
                                                                            
 Copyright (c) 2013-2022 Pavlo O. Dral                   
@@ -123,7 +123,7 @@ Cite as:
 
 1. Pavlo O. Dral, J. Comput. Chem. 2019, 40, 2339-2347             
 2. Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr, Jianxing Huang, Mario Barbatti, Top. Curr. Chem. 2021, 379, 27              
-3. Pavlo O. Dral, Peikun Zheng, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr, MLatom: A Package for Atomistic Simulations with Machine Learning, version 2.1.3, Xiamen University, Xiamen, China, 2013-2022.               
+3. Pavlo O. Dral, Peikun Zheng, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr, MLatom: A Package for Atomistic Simulations with Machine Learning, version 2.2.1, Xiamen University, Xiamen, China, 2013-2022.               
 
 
 # License

{MLatom-2.1.3 → MLatom-2.2.1}/setup.py

@@ -43,7 +43,7 @@ with open(os.path.join(here, 'README.md')) as f:
 
 setup(
     name = pkg_name,
-    version = "2.1.3",
+    version = "2.2.1",
     author = "Pavlo O. Dral",
     author_email = "admin@mlatom.com",
     license = 'CC BY-NC-ND 4.0',  # https://creativecommons.org/licenses/by-nc-nd/4.0/
@@ -55,7 +55,7 @@ setup(
     packages = find_packages('src'),
     package_dir = {'' : 'src'},
     # scripts = ['mlatom', 'MLatomF'],
-    package_data = {"": ['MLatomF', '*.json', 'cs.so', '*.pt']},
+    package_data = {"": ['MLatomF', 'README', '*.json', 'cs.so', '*.pt', '*.dat', '*.txt', '*.inp', '*.saved', '*.sh']},
     classifiers = [
         "Programming Language :: Python :: 3",
         "Operating System :: POSIX :: Linux",

{MLatom-2.1.3 → MLatom-2.2.1}/src/MLatom/MLatom.py

@@ -4,7 +4,7 @@
   !---------------------------------------------------------------------------!
   !                                                                           !
   !     MLatom: a Package for Atomistic Simulations with Machine Learning     !
-  !                               Version 2.1.2                               !
+  !                             Version 2.2.1                                 !
   !                           http://mlatom.com/                              !
   !                                                                           !
   !                  Copyright (c) 2013-2022 Pavlo O. Dral                    !
@@ -34,7 +34,7 @@
   ! Pavlo O. Dral, Peikun Zheng, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou,          !
   ! Max Pinheiro Jr,                                                          !
   ! MLatom: A Package for Atomistic Simulations with Machine Learning         !
-  ! version 2.1.2, Xiamen University, Xiamen, China, 2013-2022                !
+  ! version 2.2.1, Xiamen University, Xiamen, China, 2013-2022                !
   !                                                                           !  
   !---------------------------------------------------------------------------!
 

{MLatom-2.1.3 → MLatom-2.2.1}/src/MLatom/MLatomF_src/MLatomF.f90

@@ -2,10 +2,10 @@
   !---------------------------------------------------------------------------!
   !                                                                           !
   !     MLatom: a Package for Atomistic Simulations with Machine Learning     !
-  !                             Version 2.1.2                                 !
+  !                               Version 2.0                                 !
   !                           http://mlatom.com/                              !
   !                                                                           !
-  !                  Copyright (c) 2013-2022 Pavlo O. Dral                    !
+  !                  Copyright (c) 2013-2021 Pavlo O. Dral                    !
   !                           http://dr-dral.com/                             !
   !                                                                           !
   ! All rights reserved. No part of MLatom may be used, published or          !
@@ -29,7 +29,7 @@
   !                                                                           !
   ! Pavlo O. Dral, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou,                        !
   ! MLatom: A Package for Atomistic Simulations with Machine Learning         !
-  ! version 2.1.2, Xiamen University, Xiamen, China, 2013-2022                !
+  ! version 2.0, Xiamen University, Xiamen, China, 2013-2021                  !
   !                                                                           !  
   !---------------------------------------------------------------------------!
   

{MLatom-2.1.3 → MLatom-2.2.1}/src/MLatom/MLatomF_src/Makefile

@@ -24,7 +24,7 @@ all: ../MLatomF ../cs.so
 	
 # ML_NEA cross section shared object
 ../cs.so : cs.cpp
-	gcc -fPIC cs.cpp -shared -lstdc++ -fopenmp -O3 -o $@
+	gcc -fPIC cs.cpp -static-libgcc -shared -lstdc++ -fopenmp -O3 -o $@
 
 # Dependencies
 A_KRR.o : A_KRR.f90 A_KRR_kernel.o dataset.o mathUtils.o \

{MLatom-2.1.3 → MLatom-2.2.1}/src/MLatom/MLatomF_src/mathUtils.f90

@@ -23,9 +23,13 @@ subroutine invertMatrix(AA, nn)
   ! Arguments
   integer, intent(in)             :: nn
   real(kind=rprec), intent(inout) :: AA(1:nn,1:nn)
+  ! Local variable
+  integer :: Error
 
+  Error = 0
   if (option%matDecomp == 'Cholesky') then
-    call invertCholesky(AA, nn)
+    call invertCholesky(AA, nn, Error)
+    if (Error > 0) call invertBK(AA, nn)
   elseif (option%matDecomp == 'LU') then
     call invertLU(AA, nn)
   elseif (option%matDecomp == 'Bunch-Kaufman') then
@@ -106,7 +110,7 @@ end subroutine invertLU
 !==============================================================================
 
 !==============================================================================
-subroutine invertCholesky(AA, nn)
+subroutine invertCholesky(AA, nn, Error)
 !==============================================================================
 ! Subroutine return inverse of a matrix aInv and destroy passed matrix aInv
 ! It uses Cholesky factorization and MKL/Lapack subroutines
@@ -118,8 +122,9 @@ subroutine invertCholesky(AA, nn)
   ! Arguments
   integer, intent(in)             :: nn
   real(kind=rprec), intent(inout) :: AA(1:nn,1:nn)
+  integer, intent(out)            :: Error
   ! Local variables
-  integer :: ii, jj, Error
+  integer :: ii, jj
   ! Arrays
   integer*8                       :: dateStart(1:8)   ! Time and date, when MLatomF starts
 
@@ -137,7 +142,8 @@ subroutine invertCholesky(AA, nn)
       call date_and_time(values=dateStart)
     end if
   elseif (Error > 0) then
-    call stopMLatomF('invertCholesky: Cholesky factorization could not be completed')
+    write(6,'(A)') 'invertCholesky: Cholesky decomposition failed. Attempting Bunch-Kaufman decomposition'
+    return
   elseif (Error < 0) then
     call stopMLatomF('invertCholesky: Argument had an illegal value')
   end if
@@ -166,7 +172,7 @@ end subroutine invertCholesky
 !==============================================================================
 subroutine invertBK(AA, nn)
 !==============================================================================
-! Uses LU factorization and MKL/Lapack subroutines
+! Uses Bunch-Kaufman factorization and MKL/Lapack subroutines
 !==============================================================================
   use optionsModule, only : option
   use stopper,       only : stopMLatomF
@@ -246,9 +252,13 @@ subroutine solveSysLinEqs(nn, nrhs, AA, bb, xx)
   real(kind=rprec), intent(inout) :: AA(1:nn,1:nn)
   real(kind=rprec), intent(in)    :: bb(1:nn, 1:nrhs)
   real(kind=rprec), intent(out)   :: xx(1:nn, 1:nrhs)
+  ! Local variable
+  integer :: Error
 
+  Error = 0
   if (option%matDecomp == 'Cholesky') then
-    call solveSysLinEqsCholesky(nn, nrhs, AA, bb, xx)
+    call solveSysLinEqsCholesky(nn, nrhs, AA, bb, xx, Error)
+    if (Error > 0) call solveSysLinEqsBK(nn, nrhs, AA, bb, xx)
   elseif (option%matDecomp == 'LU') then
     call solveSysLinEqsLU(nn, nrhs, AA, bb, xx)
   elseif (option%matDecomp == 'Bunch-Kaufman') then
@@ -259,7 +269,7 @@ end subroutine solveSysLinEqs
 !==============================================================================
 
 !==============================================================================
-subroutine solveSysLinEqsCholesky(nn, nrhs, AA, bb, xx)
+subroutine solveSysLinEqsCholesky(nn, nrhs, AA, bb, xx, Error)
 !==============================================================================
 ! Subroutine solves a system of linear equations AA*xx = bb
 ! It uses Cholesky factorization and MKL/Lapack subroutines
@@ -274,8 +284,7 @@ subroutine solveSysLinEqsCholesky(nn, nrhs, AA, bb, xx)
   real(kind=rprec), intent(inout) :: AA(1:nn,1:nn)
   real(kind=rprec), intent(in)    :: bb(1:nn, 1:nrhs)
   real(kind=rprec), intent(out)   :: xx(1:nn, 1:nrhs)
-  ! Local variables
-  integer ::Error
+  integer, intent(out)            :: Error
   ! Arrays
   integer*8                       :: dateStart(1:8)   ! Time and date, when MLatomF starts
   integer, allocatable            :: iwork(:)
@@ -302,7 +311,9 @@ subroutine solveSysLinEqsCholesky(nn, nrhs, AA, bb, xx)
       call date_and_time(values=dateStart)
     end if
   elseif (Error > 0) then
-    call stopMLatomF('solveSysLinEqsCholesky: Cholesky factorization could not be completed')
+    write(6,'(A)') ' Cholesky decomposition failed. Attempting Bunch-Kaufman decomposition'
+    if(allocated(Aoriginal))    deallocate(Aoriginal)
+    return
   elseif (Error < 0) then
     call stopMLatomF('solveSysLinEqsCholesky: Argument had an illegal value')
   end if

{MLatom-2.1.3 → MLatom-2.2.1}/src/MLatom/MLatomF_src/optionsModule.f90

@@ -582,10 +582,14 @@ subroutine help(unit)
   write(unit,'(a)') "              9.0 [default]"
   write(unit,'(a)') "              <user-defined>"
   write(unit,'(a)') "            periodKernel  periodic kernel"
-  write(unit,'(a)') "               period     period"
+  write(unit,'(a)') "               period=R   period"
+  write(unit,'(a)') "                 1.0 [default]"
+  write(unit,'(a)') "                 <user-defined>"
   write(unit,'(a)') "            decayKernel   decaying periodic kernel"
-  write(unit,'(a)') "              period      period"
-  write(unit,'(a)') "              sigmap=S    length scale for a periodic part"
+  write(unit,'(a)') "              period=R    period"
+  write(unit,'(a)') "                 1.0 [default]"
+  write(unit,'(a)') "                 <user-defined>"
+  write(unit,'(a)') "              sigmap=R    length scale for a periodic part"
   write(unit,'(a)') "                100.0 [default]"
   write(unit,'(a)') "                <user-defined>"
   write(unit,'(a)') "         Laplacian. Subsuboptions:"

{MLatom-2.1.3 → MLatom-2.2.1}/src/MLatom/README

@@ -1,5 +1,5 @@
 MLatom: a Package for Atomistic Simulations with Machine Learning
-Version 2.1.2
+Version 2.1.1
 http://mlatom.com/
 
 Copyright (c) 2013-2022 Pavlo O. Dral
@@ -15,7 +15,7 @@ Cite as:
 
 1. Pavlo O. Dral, J. Comput. Chem. 2019, 40, 2339-2347
 2. Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr, Jianxing Huang, Mario Barbatti, Top. Curr. Chem. 2021, 379, 27
-3. Pavlo O. Dral, Peikun Zheng, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr, MLatom: A Package for Atomistic Simulations with Machine Learning, version 2.1.2, Xiamen University, Xiamen, China, 2013-2022.
+3. Pavlo O. Dral, Peikun Zheng, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr, MLatom: A Package for Atomistic Simulations with Machine Learning, version 2.2, Xiamen University, Xiamen, China, 2013-2022.
 
 In addition to above citations in the published work, the users have to cite the relevant literature for the MLatom features used. Examples of suggested citations are provided on http://mlatom.com/features page in form of web links and in the output of MLatom.
 

{MLatom-2.1.3 → MLatom-2.2.1}/src/MLatom/doc.py

@@ -609,7 +609,9 @@ class Doc():
 
   Optional arguments:  
     kernel=S                   kernel function type S
-      Gaussian [default]   
+      Gaussian [default]
+        periodKernel           periodic kernel
+        decayKernel            decaying periodic kernel
       Laplacian
       exponential
       Matern
@@ -634,6 +636,11 @@ class Doc():
         lgSigmaH=R             highest value of log2(lambda)
                                [default values:  9.0 (Gaussian  & Matern)
                                                 12.0 (Laplacian & exponential)]
+    period                     period in periodic and decayed periodic kernel
+                               [1.0 by default]
+    sigmap=R                   length scale for a periodic part
+                               in decayed periodic kernel
+                               [100.0 by default]
     matDecomp=S                type of matrix decomposition
       Cholesky [default]
       LU                   

{MLatom-2.1.3 → MLatom-2.2.1}/src/MLatom/example/mlatom.saved

@@ -3,14 +3,16 @@
   !---------------------------------------------------------------------------!
   !                                                                           !
   !     MLatom: a Package for Atomistic Simulations with Machine Learning     !
-  !                               Version 2.0                                 !
+  !                               Version 2.2                                 !
   !                           http://mlatom.com/                              !
   !                                                                           !
-  !                  Copyright (c) 2013-2021 Pavlo O. Dral                    !
+  !                  Copyright (c) 2013-2022 Pavlo O. Dral                    !
   !                           http://dr-dral.com/                             !
   !                                                                           !
-  ! All rights reserved. No part of MLatom may be used, published or          !
-  ! redistributed without written permission by Pavlo Dral.                   ! 
+  ! All rights reserved. This work is licensed under the                      !
+  ! Attribution-NonCommercial-NoDerivatives 4.0 International                 ! 
+  ! (http://creativecommons.org/licenses/by-nc-nd/4.0/) license.              !
+  ! See LICENSE.CC-BY-NC-ND-4.0.                                              !
   !                                                                           !
   ! The above copyright notice and this permission notice shall be included   !
   ! in all copies or substantial portions of the Software.                    !
@@ -26,19 +28,20 @@
   !                                Cite as:                                   !
   ! Pavlo O. Dral, J. Comput. Chem. 2019, 40, 2339-2347                       !
   ! Pavlo O. Dral, Fuchun Ge, Bao-Xin Xue, Yi-Fan Hou, Max Pinheiro Jr,       !
-  ! Jianxing Huang, Mario Barbatti, Top. Curr. Chem. 2021, 379, 27
+  ! Jianxing Huang, Mario Barbatti, Top. Curr. Chem. 2021, 379, 27            !
   !                                                                           !
-  ! Pavlo O. Dral, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou, Max Pinheiro Jr,       !
+  ! Pavlo O. Dral, Peikun Zheng, Bao-Xin Xue, Fuchun Ge, Yi-Fan Hou,          !
+  ! Max Pinheiro Jr,                                                          !
   ! MLatom: A Package for Atomistic Simulations with Machine Learning         !
-  ! version 2.0, Xiamen University, Xiamen, China, 2013-2021                  !
+  ! version 2.2, Xiamen University, Xiamen, China, 2013-2022                  !
   !                                                                           !  
   !---------------------------------------------------------------------------!
 
 
  ============================================================================== 
- MLatom started on 10.09.2021 at 08:33:54
+ MLatom started on 18.04.2022 at 12:20:53
         with the following options:
-        ../bin/MLatom.py mlatom.inp
+        ../MLatom.py mlatom.inp
 
         Input file content:
  ______________________________________________________________________________ 
@@ -72,6 +75,7 @@ iTrainIn=itrain.dat iTestIn=itest.dat iSubtrainIn=isubtrain.dat iValidateIn=ival
    J. Chem. Theory Comput. 2015, 11, 2087
 
  ****************************************************************************** 
+> /home/dral/soft/MLatom/releases/MLatom2.0_rev433_20210219/delete/bla/MLatom_v2.2/MLatomF estAccMLmodel XfileIn=R_451.dat YestFile=corr_ML_451.dat Ntrain=17 Nsubtrain=13 iTrainIn=itrain.dat iTestIn=itest.dat iSubtrainIn=isubtrain.dat iValidateIn=ivalidate.dat sampling=user-defined kernel=Gaussian sigma=opt lgSigmaL=-10 lgSigmaH=10 lambda=opt lgLambdaL=-40 lgOptDepth=2 NlgSigma=11 Yfile=E_FCI_451-E_UHF_451.dat
 
   !---------------------------------------------------------------------------! 
   ! MLatomF: Fortran + OpenMP part of MLatom                                  ! 
@@ -79,7 +83,7 @@ iTrainIn=itrain.dat iTestIn=itest.dat iSubtrainIn=isubtrain.dat iValidateIn=ival
   !---------------------------------------------------------------------------! 
 
 
- MLatomF started on 10.09.2021 at 08:33:54
+ MLatomF started on 18.04.2022 at 12:20:53
 
  ___________________________________________________________
 
@@ -121,6 +125,7 @@ iTrainIn=itrain.dat iTestIn=itest.dat iSubtrainIn=isubtrain.dat iValidateIn=ival
         NlgSigma:          11
         lgSigmaL:          -10
         lgSigmaH:          10
+      prior:               0
     Program run options:
       Cholesky decomposition
                            calculate and store kernel matrix
@@ -234,12 +239,12 @@ iTrainIn=itrain.dat iTestIn=itest.dat iSubtrainIn=isubtrain.dat iValidateIn=ival
      reference value =          -0.1212101000000
 
 
- Wall-clock time:       0.08 sec
+ Wall-clock time:       0.06 sec
 
- MLatomF terminated on 10.09.2021 at 08:33:54
+ MLatomF terminated on 18.04.2022 at 12:20:53
 
  ============================================================================== 
  Wall-clock time: 0.10 s (0.00 min, 0.00 hours)
 
- MLatom terminated on 10.09.2021 at 08:33:54
+ MLatom terminated on 18.04.2022 at 12:20:53
  ============================================================================== 

{MLatom-2.1.3 → MLatom-2.2.1}/src/MLatom/example/test.sh

@@ -4,7 +4,7 @@
 # ok with a compilation of MLatom
 #
 
-mlatom='../bin/MLatom.py'
+mlatom='../MLatom.py' # You may need to adapt it to the path with MLatom.py (if you install from zipped file) or mlatom (if you install via pip)
 
 rm -f corr_ML_451.dat E_D-ML_451.dat E_FCI_451-E_UHF_451.dat
 $mlatom mlatom.inp > mlatom.out

{MLatom-2.1.3 → MLatom-2.2.1}/src/MLatom/header.py

@@ -80,6 +80,12 @@ def printHeader(args):
         elif 'optprog=gaussian' in ' '.join(args.args2pass).lower():
             refItems['Gaussian program']  = refs['Gaussian']
     
+    if 'periodkernel' in ' '.join(args.args2pass).lower():
+        refItems['Periodic kernel'] = refs['4D'] + '\n\n' + refs['sklpaper']
+
+    if 'decaykernel' in ' '.join(args.args2pass).lower():
+        refItems['Decaying periodic kernel'] = refs['MLQDSBbench'] + '\n\n' + refs['sklpaper'] + '\n\n' + refs['RasmussenGP']
+    
     # Data set tasks
     if args.sampleFromSlices or args.mergeSlices or args.slice: refItems['slicing'] = refs['JCP2017_MLCH3Cl']
     if args.sampling == 'structure-based': refItems['structure-based sampling'] = refs['JCP2017_MLCH3Cl']