Merge pull request #27 from sntioudis/main

Merge for version 2.0.0
sntioudis · Sep 17, 2024 · 24ca6a3 · 24ca6a3
2 parents 9e75499 + 9b7a21c
commit 24ca6a3
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diff --git a/.github/workflows/build-reusable.yml b/.github/workflows/build-reusable.yml
@@ -24,6 +24,9 @@ jobs:
 
     steps:
 
+    - name: checkout PAPRECA
+      uses: actions/checkout@v4 #Checkout PAPRECA repository (to retrieve headers and source files for papreca fix) in case LAMMPS needs building.
+
     - name: Clone a specific LAMMPS branch
       if: ${{ inputs.clone_type == 'branch' }}
       run: |
@@ -63,11 +66,13 @@ jobs:
         sudo apt-get update
         sudo apt-get install -y build-essential
         sudo apt-get install mpich
-        
+      
     - name: Configure and build LAMMPS
       if: ${{ steps.cache-lammps-repo.outputs.cache-hit != 'true' }}
       run: |
         cd mylammps
+        cp $GITHUB_WORKSPACE/source/libraries/LAMMPS/fix_papreca.h ./src/
+        cp $GITHUB_WORKSPACE/source/libraries/LAMMPS/fix_papreca.cpp ./src/
         mkdir build; cd build
         cmake -DPKG_KOKKOS=on -DPKG_KSPACE=on -DPKG_MOLECULE=on -DPKG_RIGID=on -DPKG_QEQ=on -DBUILD_LIB=on -DBUILD_SHARED_LIBS=on ../cmake #Configure LAMMPS, build all required packages to run tests and enable static library building
         cmake --build .

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -1,7 +1,10 @@
 name: Documentation
 
 on:
-  workflow_dispatch: #Only trigger manually
+  workflow_dispatch: #Trigger manually (from main branch) OR whenever there are pushes on the release branch
+  push:
+    branches:
+        -release
 
 jobs:
   build-documentation:

diff --git a/Examples/Brownian Self Diffusion/in_kmc.lmp b/Examples/Brownian Self Diffusion/in_kmc.lmp
@@ -4,7 +4,7 @@
 dimension 3
 units           real
 atom_style      full
-pair_style 	hybrid/overlay lj/cut 10 zero 10 full
+pair_style 		lj/cut 10
 
 #---------------------------Processors-------------------------------------
 processors * * *
@@ -15,15 +15,15 @@ boundary p p p
 region simulation_box block -150 150 -150 150 -150 150
 create_box 1 simulation_box
 
+#--------------------------PAPRECA fix-------------------------------
+fix papreca all papreca
 #--------------------------Create atoms------------
 region origin_sphere sphere 0.0 0.0 0.0 20
 create_atoms 1 random 300 141241 origin_sphere overlap 1
 #---------------------------Atom masses------------------------------------
 mass 1    1.0079
 #----------------------Pair coeffs -------------------------
-pair_coeff 1 1 lj/cut 0.0152 2.84642
-
-pair_coeff * * zero
+pair_coeff 1 1 0.0152 2.84642 10.0
 #----------------------Define group and neib/charge interactions-----------
 neighbor        2 bin
 neigh_modify    every 1 delay 0 check yes

diff --git a/Examples/Brownian Self Diffusion/in_kmc.ppc b/Examples/Brownian Self Diffusion/in_kmc.ppc
@@ -7,7 +7,7 @@ random_seed 13452234
 fluid_atomtypes 1 1
 
 #Sigmas for types
-sigmas_options LAMMPS mix geom
+sigmas_options LAMMPS
 
 #Equilibration
 trajectory_duration 1
@@ -16,9 +16,6 @@ trajectory_duration 1
 create_DiffusionHop 1 0.0 3 yes 1 rate_manual 1.0
 random_diffvecs yes 3D
 
-#NeibLists
-neiblists lj/cut zero
-
 #Export files
 export_ElementalDistributions 1000 bin_width 10
 export_ExecutionTimes 1000
diff --git a/Examples/Brownian Self Diffusion/test_brownian.sh b/Examples/Brownian Self Diffusion/test_brownian.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-papreca_dir="../../build"
+papreca_dir="../../build/PAPRECA/"
 
 #Run test
 mpiexec "${papreca_dir}/papreca" -in in_kmc.lmp in_kmc.ppc

diff --git a/Examples/Phosphate Film Growth from TCP on Fe110/in_kmc.lmp b/Examples/Phosphate Film Growth from TCP on Fe110/in_kmc.lmp
@@ -2,7 +2,7 @@
 dimension 3
 units           real
 atom_style      full
-pair_style 		hybrid/overlay lj/cut/coul/cut 10 zero 10 full
+pair_style 		lj/cut/coul/cut 10
 bond_style      harmonic
 angle_style     harmonic
 dihedral_style  harmonic
@@ -17,6 +17,9 @@ boundary p p mm
 region simulation_box block -29.372 29.372 -29.66 29.66 0 60
 create_box 8 simulation_box bond/types 12 angle/types 4 dihedral/types 22 improper/types 3 extra/bond/per/atom 6 extra/angle/per/atom 6 extra/dihedral/per/atom 14 extra/improper/per/atom 2 extra/special/per/atom 7
 
+#---------------------------Fix papreca---------------------------
+fix papreca all papreca
+
 #--------------------------Create surface atoms------------
 lattice fcc 2.866 origin 0.0 0.0 0.0 orient x 1 -1 0 orient y 0 0 -2 orient z 1 1 0 #Miller indices set so that the z-axis is collinear to the 1 1 0 crystallographic direction (this enables growth on FCC 110)
 region substrate block -29 29 -29 29 0.0 2.02657 units box
@@ -32,191 +35,16 @@ mass 7    1.0079 #H
 mass 8   55.8450 #Fe
 
 #----------------------Pair coeffs -------------------------
-pair_coeff 1 1 lj/cut/coul/cut 0.055 4.04468
-
-pair_coeff 1 2 lj/cut/coul/cut 0.07505 3.74795
-pair_coeff 2 1 lj/cut/coul/cut 0.07505 3.74795
-
-pair_coeff 1 3 lj/cut/coul/cut 0.07505 3.74795
-pair_coeff 3 1 lj/cut/coul/cut 0.07505 3.74795
-
-pair_coeff 1 4 lj/cut/coul/cut 0.07535 3.50259
-pair_coeff 4 1 lj/cut/coul/cut 0.07535 3.50259
-
-pair_coeff 1 5 lj/cut/coul/cut 0.1875 3.86705
-pair_coeff 5 1 lj/cut/coul/cut 0.1875 3.86705
-
-pair_coeff 1 6 lj/cut/coul/cut 0.07535 3.50259
-pair_coeff 6 1 lj/cut/coul/cut 0.07535 3.50259
-
-pair_coeff 1 7 lj/cut/coul/cut 0.0351 3.39306
-pair_coeff 7 1 lj/cut/coul/cut 0.0351 3.39306
-
-pair_coeff 1 8 lj/cut/coul/cut 0.055 4.04468
-pair_coeff 8 1 lj/cut/coul/cut 0.055 4.04468
-
-pair_coeff 2 1 lj/cut/coul/cut 0.07505 3.74795
-pair_coeff 1 2 lj/cut/coul/cut 0.07505 3.74795
-
-pair_coeff 2 2 lj/cut/coul/cut 0.0951 3.47299
-
-pair_coeff 2 3 lj/cut/coul/cut 0.0951 3.47299
-pair_coeff 3 2 lj/cut/coul/cut 0.0951 3.47299
-
-pair_coeff 2 4 lj/cut/coul/cut 0.0954 3.24563
-pair_coeff 4 2 lj/cut/coul/cut 0.0954 3.24563
-
-pair_coeff 2 5 lj/cut/coul/cut 0.20755 3.58336
-pair_coeff 5 2 lj/cut/coul/cut 0.20755 3.58336
-
-pair_coeff 2 6 lj/cut/coul/cut 0.0954 3.24563
-pair_coeff 6 2 lj/cut/coul/cut 0.0954 3.24563
-
-pair_coeff 2 7 lj/cut/coul/cut 0.05515 3.14414
-pair_coeff 7 2 lj/cut/coul/cut 0.05515 3.14414
-
-pair_coeff 2 8 lj/cut/coul/cut 0.07505 3.74795
-pair_coeff 8 2 lj/cut/coul/cut 0.07505 3.74795
-
-pair_coeff 3 1 lj/cut/coul/cut 0.07505 3.74795
-pair_coeff 1 3 lj/cut/coul/cut 0.07505 3.74795
-
-pair_coeff 3 2 lj/cut/coul/cut 0.0951 3.47299
-pair_coeff 2 3 lj/cut/coul/cut 0.0951 3.47299
-
-pair_coeff 3 3 lj/cut/coul/cut 0.0951 3.47299
-
-pair_coeff 3 4 lj/cut/coul/cut 0.0954 3.24563
-pair_coeff 4 3 lj/cut/coul/cut 0.0954 3.24563
-
-pair_coeff 3 5 lj/cut/coul/cut 0.20755 3.58336
-pair_coeff 5 3 lj/cut/coul/cut 0.20755 3.58336
-
-pair_coeff 3 6 lj/cut/coul/cut 0.0954 3.24563
-pair_coeff 6 3 lj/cut/coul/cut 0.0954 3.24563
-
-pair_coeff 3 7 lj/cut/coul/cut 0.05515 3.14414
-pair_coeff 7 3 lj/cut/coul/cut 0.05515 3.14414
-
-pair_coeff 3 8 lj/cut/coul/cut 0.07505 3.74795
-pair_coeff 8 3 lj/cut/coul/cut 0.07505 3.74795
-
-pair_coeff 4 1 lj/cut/coul/cut 0.07535 3.50259
-pair_coeff 1 4 lj/cut/coul/cut 0.07535 3.50259
-
-pair_coeff 4 2 lj/cut/coul/cut 0.0954 3.24563
-pair_coeff 2 4 lj/cut/coul/cut 0.0954 3.24563
-
-pair_coeff 4 3 lj/cut/coul/cut 0.0954 3.24563
-pair_coeff 3 4 lj/cut/coul/cut 0.0954 3.24563
-
-pair_coeff 4 4 lj/cut/coul/cut 0.0957 3.03315
-
-pair_coeff 4 5 lj/cut/coul/cut 0.20785 3.34877
-pair_coeff 5 4 lj/cut/coul/cut 0.20785 3.34877
-
-pair_coeff 4 6 lj/cut/coul/cut 0.0957 3.03315
-pair_coeff 6 4 lj/cut/coul/cut 0.0957 3.03315
-
-pair_coeff 4 7 lj/cut/coul/cut 0.05545 2.9383
-pair_coeff 7 4 lj/cut/coul/cut 0.05545 2.9383
-
-pair_coeff 4 8 lj/cut/coul/cut 0.07535 3.50259
-pair_coeff 8 4 lj/cut/coul/cut 0.07535 3.50259
-
-pair_coeff 5 1 lj/cut/coul/cut 0.1875 3.86705
-pair_coeff 1 5 lj/cut/coul/cut 0.1875 3.86705
-
-pair_coeff 5 2 lj/cut/coul/cut 0.20755 3.58336
-pair_coeff 2 5 lj/cut/coul/cut 0.20755 3.58336
-
-pair_coeff 5 3 lj/cut/coul/cut 0.20755 3.58336
-pair_coeff 3 5 lj/cut/coul/cut 0.20755 3.58336
-
-pair_coeff 5 4 lj/cut/coul/cut 0.20785 3.34877
-pair_coeff 4 5 lj/cut/coul/cut 0.20785 3.34877
-
-pair_coeff 5 5 lj/cut/coul/cut 0.32 3.69723
-
-pair_coeff 5 6 lj/cut/coul/cut 0.20785 3.34877
-pair_coeff 6 5 lj/cut/coul/cut 0.20785 3.34877
-
-pair_coeff 5 7 lj/cut/coul/cut 0.1676 3.24405
-pair_coeff 7 5 lj/cut/coul/cut 0.1676 3.24405
-
-pair_coeff 5 8 lj/cut/coul/cut 0.1875 3.86705
-pair_coeff 8 5 lj/cut/coul/cut 0.1875 3.86705
-
-pair_coeff 6 1 lj/cut/coul/cut 0.07535 3.50259
-pair_coeff 1 6 lj/cut/coul/cut 0.07535 3.50259
-
-pair_coeff 6 2 lj/cut/coul/cut 0.0954 3.24563
-pair_coeff 2 6 lj/cut/coul/cut 0.0954 3.24563
-
-pair_coeff 6 3 lj/cut/coul/cut 0.0954 3.24563
-pair_coeff 3 6 lj/cut/coul/cut 0.0954 3.24563
-
-pair_coeff 6 4 lj/cut/coul/cut 0.0957 3.03315
-pair_coeff 4 6 lj/cut/coul/cut 0.0957 3.03315
-
-pair_coeff 6 5 lj/cut/coul/cut 0.20785 3.34877
-pair_coeff 5 6 lj/cut/coul/cut 0.20785 3.34877
-
-pair_coeff 6 6 lj/cut/coul/cut 0.0957 3.03315
-
-pair_coeff 6 7 lj/cut/coul/cut 0.05545 2.9383
-pair_coeff 7 6 lj/cut/coul/cut 0.05545 2.9383
-
-pair_coeff 6 8 lj/cut/coul/cut 0.07535 3.50259
-pair_coeff 8 6 lj/cut/coul/cut 0.07535 3.50259
-
-pair_coeff 7 1 lj/cut/coul/cut 0.0351 3.39306
-pair_coeff 1 7 lj/cut/coul/cut 0.0351 3.39306
-
-pair_coeff 7 2 lj/cut/coul/cut 0.05515 3.14414
-pair_coeff 2 7 lj/cut/coul/cut 0.05515 3.14414
-
-pair_coeff 7 3 lj/cut/coul/cut 0.05515 3.14414
-pair_coeff 3 7 lj/cut/coul/cut 0.05515 3.14414
-
-pair_coeff 7 4 lj/cut/coul/cut 0.05545 2.9383
-pair_coeff 4 7 lj/cut/coul/cut 0.05545 2.9383
-
-pair_coeff 7 5 lj/cut/coul/cut 0.1676 3.24405
-pair_coeff 5 7 lj/cut/coul/cut 0.1676 3.24405
-
-pair_coeff 7 6 lj/cut/coul/cut 0.05545 2.9383
-pair_coeff 6 7 lj/cut/coul/cut 0.05545 2.9383
-
-pair_coeff 7 7 lj/cut/coul/cut 0.0152 2.84642
-
-pair_coeff 7 8 lj/cut/coul/cut 0.0351 3.39306
-pair_coeff 8 7 lj/cut/coul/cut 0.0351 3.39306
-
-pair_coeff 8 1 lj/cut/coul/cut 0.055 4.04468
-pair_coeff 1 8 lj/cut/coul/cut 0.055 4.04468
-
-pair_coeff 8 2 lj/cut/coul/cut 0.07505 3.74795
-pair_coeff 2 8 lj/cut/coul/cut 0.07505 3.74795
-
-pair_coeff 8 3 lj/cut/coul/cut 0.07505 3.74795
-pair_coeff 3 8 lj/cut/coul/cut 0.07505 3.74795
-
-pair_coeff 8 4 lj/cut/coul/cut 0.07535 3.50259
-pair_coeff 4 8 lj/cut/coul/cut 0.07535 3.50259
-
-pair_coeff 8 5 lj/cut/coul/cut 0.1875 3.86705
-pair_coeff 5 8 lj/cut/coul/cut 0.1875 3.86705
-
-pair_coeff 8 6 lj/cut/coul/cut 0.07535 3.50259
-pair_coeff 6 8 lj/cut/coul/cut 0.07535 3.50259
-
-pair_coeff 8 7 lj/cut/coul/cut 0.0351 3.39306
-pair_coeff 7 8 lj/cut/coul/cut 0.0351 3.39306
-
-pair_coeff 8 8 lj/cut/coul/cut 0.055 4.04468
-
-pair_coeff * * zero
+pair_coeff	1	1	0.055	4.04468	10
+pair_coeff	2	2	0.0951	3.47299	10
+pair_coeff	3	3	0.0951	3.47299	10
+pair_coeff	4	4	0.0957	3.03315	10
+pair_coeff	5	5	0.32	3.69723	10
+pair_coeff	6	6	0.0957 3.03315 10
+pair_coeff	7	7	0.0152	2.84642	10
+pair_coeff	8	8	0.055	4.04468	10
+
+pair_modify mix geometric
 #---------------------------Bond coeffs-----------------------------------
 bond_coeff   1    0.00000000      0.000000    #DUMMY TYPE USED FOR BOND DELETIONS
 bond_coeff   2    350.000000      1.460000    # C_3 C_R
@@ -265,6 +93,7 @@ improper_coeff   2    20.000000     0.000000    #  C_R X X X
 improper_coeff   1    0.000000      0.000000    #  C_3 X X X 
 improper_coeff   3    0.000000      0.000000    #  P_3 X X X
 
+
 #----------------------Define Molecule Template(s)-------------------------
 molecule mmmTCP ./TCP.in
 #----------------------Define group and neib/charge interactions-------------------------

diff --git a/Examples/Phosphate Film Growth from TCP on Fe110/in_kmc.ppc b/Examples/Phosphate Film Growth from TCP on Fe110/in_kmc.ppc
@@ -12,15 +12,7 @@ height_calculation mass_bins 0.94 1.0
 desorption 20 LAMMPS_region
 
 #Sigmas for types
-sigmas_options manual mix geom
-init_sigma 1 1 4.04468
-init_sigma 2 2 3.47299
-init_sigma 3 3 3.47299
-init_sigma 4 4 3.03315
-init_sigma 5 5 3.69723
-init_sigma 6 6 3.03315
-init_sigma 7 7 2.84642
-init_sigma 8 8 4.04468
+sigmas_options LAMMPS
 
 #Species bonds max
 species_maxbonds 1 3 #Fe surface
@@ -42,9 +34,6 @@ minimize_prior yes minimize 1.0e-3 1.0e-5 100 1000
 minimize_after yes minimize 1.0e-3 1.0e-5 100 1000
 trajectory_duration 200
 
-#NeibLists
-neiblists lj/cut/coul/cut zero
-
 #Predefined events
 #!BondBreaks
 create_BondBreak 4 5 7 rate_arrhenius 13.68 6.99e10 528.15 catalyzed 2 1 8 #O_3 P_3
@@ -78,4 +67,4 @@ random_depovecs no
 #File Exports
 export_HeightVtime 10
 export_ElementalDistributions 500 bin_width 1.0
-export_ExecutionTimes 1
+export_ExecutionTimes 1
diff --git a/Examples/Phosphate Film Growth from TCP on Fe110/test_phosphates.sh b/Examples/Phosphate Film Growth from TCP on Fe110/test_phosphates.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-papreca_dir="../..//build"
+papreca_dir="../../build/PAPRECA/"
 
 #Run test
 mpiexec -np 16 "${papreca_dir}/papreca" -in in_kmc.lmp in_kmc.ppc
diff --git a/Examples/Simple Adsorption/template/in_kmc.lmp b/Examples/Simple Adsorption/template/in_kmc.lmp
@@ -4,7 +4,7 @@
 dimension 3
 units           real
 atom_style      full
-pair_style 	hybrid/overlay lj/cut 10 zero 10 full
+pair_style	   lj/cut 10
 bond_style      harmonic
 
 #---------------------------Processors----------------------------------------
@@ -16,6 +16,8 @@ boundary p p mm
 region simulation_box block -29.372 29.372 -29.66 29.66 0 60
 create_box 2 simulation_box
 
+#--------------------------PAPRECA fix--------------------------------
+fix papreca all papreca
 #--------------------------Create surface atoms------------
 lattice fcc 4.5 origin 0.0 0.0 0.0
 region substrate block -29 29 -29 29 0.0 0.5 units box
@@ -25,15 +27,10 @@ create_atoms 1 region substrate
 mass 1   55.8450
 mass 2   15.9994
 #----------------------Pair coeffs -------------------------
-pair_coeff 1 1 lj/cut 0.055 4.04468
-
-pair_coeff 1 2 lj/cut 0.07535 3.50259
-pair_coeff 2 1 lj/cut 0.07535 3.50259
-
-pair_coeff 2 2 lj/cut 0.0957 3.03315
-
-pair_coeff * * zero
+pair_coeff 1 1 0.055 4.04468 10.0
+pair_coeff 2 2 0.0957 3.03315 10.0
 
+pair_modify mix geometric
 #----------------------Define Molecule Template(s)-------------------------
 molecule particle ./particle.in