From c8ac4a8b923fea9f471e0c577625d2e7f3fd4743 Mon Sep 17 00:00:00 2001
From: Rafael Ravedutti <rafaelravedutti@gmail.com>
Date: Tue, 12 Oct 2021 00:25:07 +0200
Subject: [PATCH] Apply proper changes for pairs to be used as a package
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
---
LICENSE | 21 +
examples/kernels | 834 ++++++++++++++++++
examples/kernels.pdf | Bin 0 -> 46823 bytes
lift.py => examples/lift.py | 0
particle.py => examples/lj_embedded.py | 17 +-
examples/lj_func.py | 45 +
examples/lj_ns.cpp | 825 +++++++++++++++++
pyproject.toml | 6 +
setup.py | 46 +
{code_gen => src}/__init__.py | 0
pairs.py => src/pairs/__init__.py | 4 +-
{coupling => src/pairs/code_gen}/__init__.py | 0
{code_gen => src/pairs/code_gen}/cgen.py | 40 +-
{code_gen => src/pairs/code_gen}/printer.py | 0
{ir => src/pairs/coupling}/__init__.py | 0
{coupling => src/pairs/coupling}/parse_cpp.py | 10 +-
{sim => src/pairs/graph}/__init__.py | 0
{graph => src/pairs/graph}/graphviz.py | 14 +-
ir/operators.py => src/pairs/ir/__init__.py | 0
{ir => src/pairs/ir}/arrays.py | 16 +-
{ir => src/pairs/ir}/assign.py | 8 +-
{ir => src/pairs/ir}/ast_node.py | 2 +-
{ir => src/pairs/ir}/bin_op.py | 10 +-
{ir => src/pairs/ir}/block.py | 2 +-
{ir => src/pairs/ir}/branches.py | 6 +-
{ir => src/pairs/ir}/cast.py | 4 +-
{ir => src/pairs/ir}/data_types.py | 0
{ir => src/pairs/ir}/functions.py | 6 +-
{ir => src/pairs/ir}/layouts.py | 0
{ir => src/pairs/ir}/lit.py | 4 +-
{ir => src/pairs/ir}/loops.py | 12 +-
{ir => src/pairs/ir}/math.py | 4 +-
{ir => src/pairs/ir}/memory.py | 6 +-
{ir => src/pairs/ir}/mutator.py | 0
src/pairs/ir/operators.py | 0
{ir => src/pairs/ir}/properties.py | 14 +-
{ir => src/pairs/ir}/select.py | 6 +-
{ir => src/pairs/ir}/sizeof.py | 4 +-
{ir => src/pairs/ir}/transform.py | 14 +-
{ir => src/pairs/ir}/utils.py | 2 +-
{ir => src/pairs/ir}/variables.py | 6 +-
{ir => src/pairs/ir}/vector_expr.py | 6 +-
{ir => src/pairs/ir}/visitor.py | 0
src/pairs/mapping/.funcs.py.swp | Bin 0 -> 16384 bytes
src/pairs/mapping/__init__.py | 0
new_syntax.py => src/pairs/mapping/funcs.py | 55 +-
src/pairs/runtime/__init__.py | 0
{runtime => src/pairs/runtime}/pairs.hpp | 0
.../pairs/runtime}/read_from_file.hpp | 0
{runtime => src/pairs/runtime}/vtk.hpp | 0
src/pairs/sim/__init__.py | 0
{sim => src/pairs/sim}/arrays.py | 4 +-
{sim => src/pairs/sim}/cell_lists.py | 16 +-
{sim => src/pairs/sim}/grid.py | 2 +-
{sim => src/pairs/sim}/kernel_wrapper.py | 2 +-
{sim => src/pairs/sim}/lattice.py | 4 +-
{sim => src/pairs/sim}/neighbor_lists.py | 10 +-
{sim => src/pairs/sim}/particle_simulation.py | 56 +-
{sim => src/pairs/sim}/pbc.py | 12 +-
{sim => src/pairs/sim}/properties.py | 10 +-
{sim => src/pairs/sim}/read_from_file.py | 8 +-
{sim => src/pairs/sim}/resize.py | 12 +-
{sim => src/pairs/sim}/setup_wrapper.py | 2 +-
{sim => src/pairs/sim}/timestep.py | 8 +-
{sim => src/pairs/sim}/variables.py | 2 +-
{sim => src/pairs/sim}/vtk.py | 6 +-
.../pairs/transformations}/LICM.py | 10 +-
src/pairs/transformations/__init__.py | 0
.../transformations}/prioritize_scalar_ops.py | 6 +-
.../transformations}/set_used_bin_ops.py | 2 +-
.../pairs/transformations}/simplify.py | 6 +-
71 files changed, 1973 insertions(+), 254 deletions(-)
create mode 100644 LICENSE
create mode 100644 examples/kernels
create mode 100644 examples/kernels.pdf
rename lift.py => examples/lift.py (100%)
rename particle.py => examples/lj_embedded.py (65%)
create mode 100644 examples/lj_func.py
create mode 100644 examples/lj_ns.cpp
create mode 100644 pyproject.toml
create mode 100644 setup.py
rename {code_gen => src}/__init__.py (100%)
rename pairs.py => src/pairs/__init__.py (53%)
rename {coupling => src/pairs/code_gen}/__init__.py (100%)
rename {code_gen => src/pairs/code_gen}/cgen.py (93%)
rename {code_gen => src/pairs/code_gen}/printer.py (100%)
rename {ir => src/pairs/coupling}/__init__.py (100%)
rename {coupling => src/pairs/coupling}/parse_cpp.py (97%)
rename {sim => src/pairs/graph}/__init__.py (100%)
rename {graph => src/pairs/graph}/graphviz.py (86%)
rename ir/operators.py => src/pairs/ir/__init__.py (100%)
rename {ir => src/pairs/ir}/arrays.py (94%)
rename {ir => src/pairs/ir}/assign.py (83%)
rename {ir => src/pairs/ir}/ast_node.py (88%)
rename {ir => src/pairs/ir}/bin_op.py (96%)
rename {ir => src/pairs/ir}/block.py (97%)
rename {ir => src/pairs/ir}/branches.py (92%)
rename {ir => src/pairs/ir}/cast.py (86%)
rename {ir => src/pairs/ir}/data_types.py (100%)
rename {ir => src/pairs/ir}/functions.py (85%)
rename {ir => src/pairs/ir}/layouts.py (100%)
rename {ir => src/pairs/ir}/lit.py (88%)
rename {ir => src/pairs/ir}/loops.py (93%)
rename {ir => src/pairs/ir}/math.py (89%)
rename {ir => src/pairs/ir}/memory.py (88%)
rename {ir => src/pairs/ir}/mutator.py (100%)
create mode 100644 src/pairs/ir/operators.py
rename {ir => src/pairs/ir}/properties.py (94%)
rename {ir => src/pairs/ir}/select.py (77%)
rename {ir => src/pairs/ir}/sizeof.py (69%)
rename {ir => src/pairs/ir}/transform.py (92%)
rename {ir => src/pairs/ir}/utils.py (82%)
rename {ir => src/pairs/ir}/variables.py (93%)
rename {ir => src/pairs/ir}/vector_expr.py (92%)
rename {ir => src/pairs/ir}/visitor.py (100%)
create mode 100644 src/pairs/mapping/.funcs.py.swp
create mode 100644 src/pairs/mapping/__init__.py
rename new_syntax.py => src/pairs/mapping/funcs.py (75%)
create mode 100644 src/pairs/runtime/__init__.py
rename {runtime => src/pairs/runtime}/pairs.hpp (100%)
rename {runtime => src/pairs/runtime}/read_from_file.hpp (100%)
rename {runtime => src/pairs/runtime}/vtk.hpp (100%)
create mode 100644 src/pairs/sim/__init__.py
rename {sim => src/pairs/sim}/arrays.py (82%)
rename {sim => src/pairs/sim}/cell_lists.py (93%)
rename {sim => src/pairs/sim}/grid.py (97%)
rename {sim => src/pairs/sim}/kernel_wrapper.py (87%)
rename {sim => src/pairs/sim}/lattice.py (95%)
rename {sim => src/pairs/sim}/neighbor_lists.py (89%)
rename {sim => src/pairs/sim}/particle_simulation.py (82%)
rename {sim => src/pairs/sim}/pbc.py (94%)
rename {sim => src/pairs/sim}/properties.py (84%)
rename {sim => src/pairs/sim}/read_from_file.py (81%)
rename {sim => src/pairs/sim}/resize.py (84%)
rename {sim => src/pairs/sim}/setup_wrapper.py (87%)
rename {sim => src/pairs/sim}/timestep.py (91%)
rename {sim => src/pairs/sim}/variables.py (85%)
rename {sim => src/pairs/sim}/vtk.py (84%)
rename {transformations => src/pairs/transformations}/LICM.py (97%)
create mode 100644 src/pairs/transformations/__init__.py
rename {transformations => src/pairs/transformations}/prioritize_scalar_ops.py (93%)
rename {transformations => src/pairs/transformations}/set_used_bin_ops.py (93%)
rename {transformations => src/pairs/transformations}/simplify.py (90%)
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..5f40490
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Rafael Ravedutti Lucio Machado
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/examples/kernels b/examples/kernels
new file mode 100644
index 0000000..6fcb7d8
--- /dev/null
+++ b/examples/kernels
@@ -0,0 +1,834 @@
+digraph AST {
+ node [color=lightblue2 style=filled]
+ size="6,6"
+ n139866028692368 [label=Block]
+ n139866028640632 [label=ParticleFor]
+ n139866028692368 -> n139866028640632
+ n139866028694664 [label=ParticleFor]
+ n139866028692368 -> n139866028694664
+ n139866028640632 [label=ParticleFor]
+ n139866028694720 [label="Iter(0)"]
+ n139866028640632 -> n139866028694720
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+ n139866028695336 -> n139866028694720
+ n139866028691808 [label=neighborlist_capacity]
+ n139866028695336 -> n139866028691808
+ n139866028691808 [label=neighborlist_capacity]
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+ n139866028217512 -> n139866028694720
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+ n139866028218408 -> n139866028694720
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+ n139866028218576 -> n139866028218408
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+ n139866028218576 -> n139866028218632
+ n139866028218632 [label=1]
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+ n139866028694720 [label="Iter(0)"]
+ n139866028219192 -> n139866028694720
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+ n139866028219360 -> n139866028219192
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+ n139866028219416 [label=1]
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+ n139866028694720 [label="Iter(0)"]
+ n139866028220200 -> n139866028694720
+ n139866028220256 [label=3]
+ n139866028220200 -> n139866028220256
+ n139866028220256 [label=3]
+ n139866028220368 [label="+"]
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+ n139866028220368 -> n139866028220200
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+ n139866028220368 -> n139866028355656
+ n139866028355656 [label=2]
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+ n139866028694720 [label="Iter(0)"]
+ n139866028356216 -> n139866028694720
+ n139866028356272 [label=3]
+ n139866028356216 -> n139866028356272
+ n139866028356272 [label=3]
+ n139866028356384 [label="+"]
+ n139866028356216 [label="*"]
+ n139866028356384 -> n139866028356216
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+ n139866028356440 [label=2]
+ n139866028359408 [label="*"]
+ n139866028694720 [label="Iter(0)"]
+ n139866028359408 -> n139866028694720
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+ n139866028359408 -> n139866028359464
+ n139866028359464 [label=3]
+ n139866028388536 [label="*"]
+ n139866028694720 [label="Iter(0)"]
+ n139866028388536 -> n139866028694720
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+ n139866028388536 -> n139866028388592
+ n139866028388592 [label=3]
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+ n139866028389712 -> n139866028694720
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+ n139866028389768 [label=3]
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+ n139866028389880 -> n139866028389712
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+ n139866028389936 [label=1]
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+ n139866028694720 [label="Iter(0)"]
+ n139866028390104 -> n139866028694720
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+ n139866028390272 -> n139866028390104
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+ n139866028391448 -> n139866028391280
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+ n139866028391672 -> n139866028694720
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+ n139866028391728 [label=3]
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+ n139866028391672 [label="*"]
+ n139866028391840 -> n139866028391672
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+ n139866028695168 [label=0]
+ n139866028695056 -> n139866028695168
+ n139866028695000 [label=ArrayAccess]
+ n139866028695056 -> n139866028695000
+ n139866028695112 [label="Iter(1)"]
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+ n139866028695448 -> n139866028695336
+ n139866028695112 [label="Iter(1)"]
+ n139866028695448 -> n139866028695112
+ n139866028216448 [label=PropertyAccess]
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+ n139866028217064 [label="*"]
+ n139866028695280 [label=ArrayAccess]
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+ n139866028218800 [label=3]
+ n139866028218744 -> n139866028218800
+ n139866028218800 [label=3]
+ n139866028218912 [label="+"]
+ n139866028218744 [label="*"]
+ n139866028218912 -> n139866028218744
+ n139866028218968 [label=1]
+ n139866028218912 -> n139866028218968
+ n139866028218968 [label=1]
+ n139866028219528 [label="*"]
+ n139866028695280 [label=ArrayAccess]
+ n139866028219528 -> n139866028695280
+ n139866028219584 [label=3]
+ n139866028219528 -> n139866028219584
+ n139866028219584 [label=3]
+ n139866028219696 [label="+"]
+ n139866028219528 [label="*"]
+ n139866028219696 -> n139866028219528
+ n139866028219752 [label=1]
+ n139866028219696 -> n139866028219752
+ n139866028219752 [label=1]
+ n139866028219920 [label="*"]
+ n139866028219080 [label=VectorAccess]
+ n139866028219920 -> n139866028219080
+ n139866028219864 [label=VectorAccess]
+ n139866028219920 -> n139866028219864
+ n139866028219080 [label=VectorAccess]
+ n139866028216560 [label="-"]
+ n139866028219080 -> n139866028216560
+ n139866028219864 [label=VectorAccess]
+ n139866028216560 [label="-"]
+ n139866028219864 -> n139866028216560
+ n139866028220032 [label="+"]
+ n139866028218240 [label="*"]
+ n139866028220032 -> n139866028218240
+ n139866028219920 [label="*"]
+ n139866028220032 -> n139866028219920
+ n139866028355768 [label="*"]
+ n139866028695280 [label=ArrayAccess]
+ n139866028355768 -> n139866028695280
+ n139866028355824 [label=3]
+ n139866028355768 -> n139866028355824
+ n139866028355824 [label=3]
+ n139866028355936 [label="+"]
+ n139866028355768 [label="*"]
+ n139866028355936 -> n139866028355768
+ n139866028355992 [label=2]
+ n139866028355936 -> n139866028355992
+ n139866028355992 [label=2]
+ n139866028356552 [label="*"]
+ n139866028695280 [label=ArrayAccess]
+ n139866028356552 -> n139866028695280
+ n139866028356608 [label=3]
+ n139866028356552 -> n139866028356608
+ n139866028356608 [label=3]
+ n139866028356720 [label="+"]
+ n139866028356552 [label="*"]
+ n139866028356720 -> n139866028356552
+ n139866028356776 [label=2]
+ n139866028356720 -> n139866028356776
+ n139866028356776 [label=2]
+ n139866028356944 [label="*"]
+ n139866028356104 [label=VectorAccess]
+ n139866028356944 -> n139866028356104
+ n139866028356888 [label=VectorAccess]
+ n139866028356944 -> n139866028356888
+ n139866028356104 [label=VectorAccess]
+ n139866028216560 [label="-"]
+ n139866028356104 -> n139866028216560
+ n139866028356888 [label=VectorAccess]
+ n139866028216560 [label="-"]
+ n139866028356888 -> n139866028216560
+ n139866028357056 [label="+"]
+ n139866028220032 [label="+"]
+ n139866028357056 -> n139866028220032
+ n139866028356944 [label="*"]
+ n139866028357056 -> n139866028356944
+ n139866028357168 [label="<"]
+ n139866028357056 [label="+"]
+ n139866028357168 -> n139866028357056
+ n139866028357224 [label=2.5]
+ n139866028357168 -> n139866028357224
+ n139866028357224 [label=2.5]
+ n139866028357336 [label=Filter]
+ n139866028357168 [label="<"]
+ n139866028357336 -> n139866028357168
+ n139866028357392 [label=Block]
+ n139866028357336 -> n139866028357392
+ n139866028357392 [label=Block]
+ n139866028359296 [label=Assign]
+ n139866028357392 -> n139866028359296
+ n139866028357728 [label="/"]
+ n139866028357784 [label=1.0]
+ n139866028357728 -> n139866028357784
+ n139866028357056 [label="+"]
+ n139866028357728 -> n139866028357056
+ n139866028357784 [label=1.0]
+ n139866028357896 [label="*"]
+ n139866028357728 [label="/"]
+ n139866028357896 -> n139866028357728
+ n139866028357728 [label="/"]
+ n139866028357896 -> n139866028357728
+ n139866028358008 [label="*"]
+ n139866028357896 [label="*"]
+ n139866028358008 -> n139866028357896
+ n139866028357728 [label="/"]
+ n139866028358008 -> n139866028357728
+ n139866028357672 [label=PropertyAccess]
+ n139866028640016 [label=force]
+ n139866028357672 -> n139866028640016
+ n139866028694720 [label="Iter(0)"]
+ n139866028357672 -> n139866028694720
+ n139866028388536 [label="*"]
+ n139866028357672 -> n139866028388536
+ n139866028390272 [label="+"]
+ n139866028357672 -> n139866028390272
+ n139866028391840 [label="+"]
+ n139866028357672 -> n139866028391840
+ n139866028640016 [label=force]
+ n139866028358344 [label="*"]
+ n139866028216560 [label="-"]
+ n139866028358344 -> n139866028216560
+ n139866028358400 [label=48.0]
+ n139866028358344 -> n139866028358400
+ n139866028358400 [label=48.0]
+ n139866028358512 [label="*"]
+ n139866028216560 [label="-"]
+ n139866028358512 -> n139866028216560
+ n139866027164896 [label="*"]
+ n139866028358512 -> n139866027164896
+ n139866027164896 [label="*"]
+ n139866028358400 [label=48.0]
+ n139866027164896 -> n139866028358400
+ n139866028358008 [label="*"]
+ n139866027164896 -> n139866028358008
+ n139866028358624 [label="-"]
+ n139866028358008 [label="*"]
+ n139866028358624 -> n139866028358008
+ n139866028358680 [label=0.5]
+ n139866028358624 -> n139866028358680
+ n139866028358680 [label=0.5]
+ n139866028358792 [label="*"]
+ n139866028216560 [label="-"]
+ n139866028358792 -> n139866028216560
+ n139866027165008 [label="*"]
+ n139866028358792 -> n139866027165008
+ n139866027165008 [label="*"]
+ n139866027164896 [label="*"]
+ n139866027165008 -> n139866027164896
+ n139866028358624 [label="-"]
+ n139866027165008 -> n139866028358624
+ n139866028358904 [label="*"]
+ n139866028216560 [label="-"]
+ n139866028358904 -> n139866028216560
+ n139866027165120 [label="*"]
+ n139866028358904 -> n139866027165120
+ n139866027165120 [label="*"]
+ n139866027165008 [label="*"]
+ n139866027165120 -> n139866027165008
+ n139866028357728 [label="/"]
+ n139866027165120 -> n139866028357728
+ n139866028359016 [label="*"]
+ n139866028216560 [label="-"]
+ n139866028359016 -> n139866028216560
+ n139866027165120 [label="*"]
+ n139866028359016 -> n139866027165120
+ n139866028359184 [label="+"]
+ n139866028357672 [label=PropertyAccess]
+ n139866028359184 -> n139866028357672
+ n139866028359016 [label="*"]
+ n139866028359184 -> n139866028359016
+ n139866028359296 [label=Assign]
+ n139866028389600 [label=VectorAccess]
+ n139866028359296 -> n139866028389600
+ n139866028388480 [label=VectorAccess]
+ n139866028359296 -> n139866028388480
+ n139866028391168 [label=VectorAccess]
+ n139866028359296 -> n139866028391168
+ n139866028390048 [label=VectorAccess]
+ n139866028359296 -> n139866028390048
+ n139866028425568 [label=VectorAccess]
+ n139866028359296 -> n139866028425568
+ n139866028391616 [label=VectorAccess]
+ n139866028359296 -> n139866028391616
+ n139866028389600 [label=VectorAccess]
+ n139866028357672 [label=PropertyAccess]
+ n139866028389600 -> n139866028357672
+ n139866028388480 [label=VectorAccess]
+ n139866028359184 [label="+"]
+ n139866028388480 -> n139866028359184
+ n139866028391168 [label=VectorAccess]
+ n139866028357672 [label=PropertyAccess]
+ n139866028391168 -> n139866028357672
+ n139866028390048 [label=VectorAccess]
+ n139866028359184 [label="+"]
+ n139866028390048 -> n139866028359184
+ n139866028425568 [label=VectorAccess]
+ n139866028357672 [label=PropertyAccess]
+ n139866028425568 -> n139866028357672
+ n139866028391616 [label=VectorAccess]
+ n139866028359184 [label="+"]
+ n139866028391616 -> n139866028359184
+ n139866028695168 [label=0]
+ n139866028695000 [label=ArrayAccess]
+ n139866028691920 [label=numneighs]
+ n139866028695000 -> n139866028691920
+ n139866028694720 [label="Iter(0)"]
+ n139866028695000 -> n139866028694720
+ n139866028691920 [label=numneighs]
+ n139866028694776 [label=0]
+ n139866028694832 [label=0]
+ n139866028694664 [label=ParticleFor]
+ n139866028693656 [label="Iter(2)"]
+ n139866028694664 -> n139866028693656
+ n139866028692592 [label=Block]
+ n139866028694664 -> n139866028692592
+ n139866028693544 [label=0]
+ n139866028694664 -> n139866028693544
+ n139866028693320 [label=0]
+ n139866028694664 -> n139866028693320
+ n139866028693656 [label="Iter(2)"]
+ n139866028692592 [label=Block]
+ n139866028426240 [label=Assign]
+ n139866028692592 -> n139866028426240
+ n139866027930848 [label=Assign]
+ n139866028692592 -> n139866027930848
+ n139866028357560 [label=PropertyAccess]
+ n139866028639960 [label=velocity]
+ n139866028357560 -> n139866028639960
+ n139866028693656 [label="Iter(2)"]
+ n139866028357560 -> n139866028693656
+ n139866028426744 [label="*"]
+ n139866028357560 -> n139866028426744
+ n139866028428480 [label="+"]
+ n139866028357560 -> n139866028428480
+ n139866027930064 [label="+"]
+ n139866028357560 -> n139866027930064
+ n139866028639960 [label=velocity]
+ n139866028426744 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866028426744 -> n139866028693656
+ n139866028427136 [label=3]
+ n139866028426744 -> n139866028427136
+ n139866028427136 [label=3]
+ n139866028428480 [label="+"]
+ n139866028427976 [label="*"]
+ n139866028428480 -> n139866028427976
+ n139866028428536 [label=1]
+ n139866028428480 -> n139866028428536
+ n139866028427976 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866028427976 -> n139866028693656
+ n139866028428368 [label=3]
+ n139866028427976 -> n139866028428368
+ n139866028428368 [label=3]
+ n139866028428536 [label=1]
+ n139866027930064 [label="+"]
+ n139866028429208 [label="*"]
+ n139866027930064 -> n139866028429208
+ n139866027930120 [label=2]
+ n139866027930064 -> n139866027930120
+ n139866028429208 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866028429208 -> n139866028693656
+ n139866027929952 [label=3]
+ n139866028429208 -> n139866027929952
+ n139866027929952 [label=3]
+ n139866027930120 [label=2]
+ n139866028425624 [label=PropertyAccess]
+ n139866028640016 [label=force]
+ n139866028425624 -> n139866028640016
+ n139866028693656 [label="Iter(2)"]
+ n139866028425624 -> n139866028693656
+ n139866028426800 [label="*"]
+ n139866028425624 -> n139866028426800
+ n139866028428200 [label="+"]
+ n139866028425624 -> n139866028428200
+ n139866027929784 [label="+"]
+ n139866028425624 -> n139866027929784
+ n139866028426800 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866028426800 -> n139866028693656
+ n139866028426856 [label=3]
+ n139866028426800 -> n139866028426856
+ n139866028426856 [label=3]
+ n139866028428200 [label="+"]
+ n139866028428032 [label="*"]
+ n139866028428200 -> n139866028428032
+ n139866028428256 [label=1]
+ n139866028428200 -> n139866028428256
+ n139866028428032 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866028428032 -> n139866028693656
+ n139866028428088 [label=3]
+ n139866028428032 -> n139866028428088
+ n139866028428088 [label=3]
+ n139866028428256 [label=1]
+ n139866027929784 [label="+"]
+ n139866028429264 [label="*"]
+ n139866027929784 -> n139866028429264
+ n139866027929840 [label=2]
+ n139866027929784 -> n139866027929840
+ n139866028429264 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866028429264 -> n139866028693656
+ n139866027929672 [label=3]
+ n139866028429264 -> n139866027929672
+ n139866027929672 [label=3]
+ n139866027929840 [label=2]
+ n139866028425736 [label="*"]
+ n139866028425792 [label=0.005]
+ n139866028425736 -> n139866028425792
+ n139866028425624 [label=PropertyAccess]
+ n139866028425736 -> n139866028425624
+ n139866028425792 [label=0.005]
+ n139866028425904 [label=PropertyAccess]
+ n139866028639848 [label=mass]
+ n139866028425904 -> n139866028639848
+ n139866028693656 [label="Iter(2)"]
+ n139866028425904 -> n139866028693656
+ n139866028639848 [label=mass]
+ n139866028426016 [label="/"]
+ n139866028425736 [label="*"]
+ n139866028426016 -> n139866028425736
+ n139866028425904 [label=PropertyAccess]
+ n139866028426016 -> n139866028425904
+ n139866028426128 [label="+"]
+ n139866028357560 [label=PropertyAccess]
+ n139866028426128 -> n139866028357560
+ n139866028426016 [label="/"]
+ n139866028426128 -> n139866028426016
+ n139866028426352 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866028426352 -> n139866028693656
+ n139866028426408 [label=3]
+ n139866028426352 -> n139866028426408
+ n139866028426408 [label=3]
+ n139866028427584 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866028427584 -> n139866028693656
+ n139866028427640 [label=3]
+ n139866028427584 -> n139866028427640
+ n139866028427640 [label=3]
+ n139866028427752 [label="+"]
+ n139866028427584 [label="*"]
+ n139866028427752 -> n139866028427584
+ n139866028427808 [label=1]
+ n139866028427752 -> n139866028427808
+ n139866028427808 [label=1]
+ n139866028428816 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866028428816 -> n139866028693656
+ n139866028428872 [label=3]
+ n139866028428816 -> n139866028428872
+ n139866028428872 [label=3]
+ n139866028428984 [label="+"]
+ n139866028428816 [label="*"]
+ n139866028428984 -> n139866028428816
+ n139866028429040 [label=2]
+ n139866028428984 -> n139866028429040
+ n139866028429040 [label=2]
+ n139866028426240 [label=Assign]
+ n139866028427472 [label=VectorAccess]
+ n139866028426240 -> n139866028427472
+ n139866028426688 [label=VectorAccess]
+ n139866028426240 -> n139866028426688
+ n139866028428704 [label=VectorAccess]
+ n139866028426240 -> n139866028428704
+ n139866028427920 [label=VectorAccess]
+ n139866028426240 -> n139866028427920
+ n139866027930288 [label=VectorAccess]
+ n139866028426240 -> n139866027930288
+ n139866028429152 [label=VectorAccess]
+ n139866028426240 -> n139866028429152
+ n139866028427472 [label=VectorAccess]
+ n139866028357560 [label=PropertyAccess]
+ n139866028427472 -> n139866028357560
+ n139866028426688 [label=VectorAccess]
+ n139866028426128 [label="+"]
+ n139866028426688 -> n139866028426128
+ n139866028428704 [label=VectorAccess]
+ n139866028357560 [label=PropertyAccess]
+ n139866028428704 -> n139866028357560
+ n139866028427920 [label=VectorAccess]
+ n139866028426128 [label="+"]
+ n139866028427920 -> n139866028426128
+ n139866027930288 [label=VectorAccess]
+ n139866028357560 [label=PropertyAccess]
+ n139866027930288 -> n139866028357560
+ n139866028429152 [label=VectorAccess]
+ n139866028426128 [label="+"]
+ n139866028429152 -> n139866028426128
+ n139866027930344 [label=PropertyAccess]
+ n139866028639904 [label=position]
+ n139866027930344 -> n139866028639904
+ n139866028693656 [label="Iter(2)"]
+ n139866027930344 -> n139866028693656
+ n139866027931688 [label="*"]
+ n139866027930344 -> n139866027931688
+ n139866027933088 [label="+"]
+ n139866027930344 -> n139866027933088
+ n139866027967152 [label="+"]
+ n139866027930344 -> n139866027967152
+ n139866027931688 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866027931688 -> n139866028693656
+ n139866027931744 [label=3]
+ n139866027931688 -> n139866027931744
+ n139866027931744 [label=3]
+ n139866027933088 [label="+"]
+ n139866027932920 [label="*"]
+ n139866027933088 -> n139866027932920
+ n139866027933144 [label=1]
+ n139866027933088 -> n139866027933144
+ n139866027932920 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866027932920 -> n139866028693656
+ n139866027932976 [label=3]
+ n139866027932920 -> n139866027932976
+ n139866027932976 [label=3]
+ n139866027933144 [label=1]
+ n139866027967152 [label="+"]
+ n139866027966984 [label="*"]
+ n139866027967152 -> n139866027966984
+ n139866027967208 [label=2]
+ n139866027967152 -> n139866027967208
+ n139866027966984 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866027966984 -> n139866028693656
+ n139866027967040 [label=3]
+ n139866027966984 -> n139866027967040
+ n139866027967040 [label=3]
+ n139866027967208 [label=2]
+ n139866027930456 [label=PropertyAccess]
+ n139866028639960 [label=velocity]
+ n139866027930456 -> n139866028639960
+ n139866028693656 [label="Iter(2)"]
+ n139866027930456 -> n139866028693656
+ n139866027931352 [label="*"]
+ n139866027930456 -> n139866027931352
+ n139866027932752 [label="+"]
+ n139866027930456 -> n139866027932752
+ n139866027966816 [label="+"]
+ n139866027930456 -> n139866027966816
+ n139866027931352 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866027931352 -> n139866028693656
+ n139866027931408 [label=3]
+ n139866027931352 -> n139866027931408
+ n139866027931408 [label=3]
+ n139866027932752 [label="+"]
+ n139866027932584 [label="*"]
+ n139866027932752 -> n139866027932584
+ n139866027932808 [label=1]
+ n139866027932752 -> n139866027932808
+ n139866027932584 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866027932584 -> n139866028693656
+ n139866027932640 [label=3]
+ n139866027932584 -> n139866027932640
+ n139866027932640 [label=3]
+ n139866027932808 [label=1]
+ n139866027966816 [label="+"]
+ n139866027966648 [label="*"]
+ n139866027966816 -> n139866027966648
+ n139866027966872 [label=2]
+ n139866027966816 -> n139866027966872
+ n139866027966648 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866027966648 -> n139866028693656
+ n139866027966704 [label=3]
+ n139866027966648 -> n139866027966704
+ n139866027966704 [label=3]
+ n139866027966872 [label=2]
+ n139866027930568 [label="*"]
+ n139866027930624 [label=0.005]
+ n139866027930568 -> n139866027930624
+ n139866027930456 [label=PropertyAccess]
+ n139866027930568 -> n139866027930456
+ n139866027930624 [label=0.005]
+ n139866027930736 [label="+"]
+ n139866027930344 [label=PropertyAccess]
+ n139866027930736 -> n139866027930344
+ n139866027930568 [label="*"]
+ n139866027930736 -> n139866027930568
+ n139866027930960 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866027930960 -> n139866028693656
+ n139866027931016 [label=3]
+ n139866027930960 -> n139866027931016
+ n139866027931016 [label=3]
+ n139866027932192 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866027932192 -> n139866028693656
+ n139866027932248 [label=3]
+ n139866027932192 -> n139866027932248
+ n139866027932248 [label=3]
+ n139866027932360 [label="+"]
+ n139866027932192 [label="*"]
+ n139866027932360 -> n139866027932192
+ n139866027932416 [label=1]
+ n139866027932360 -> n139866027932416
+ n139866027932416 [label=1]
+ n139866027933424 [label="*"]
+ n139866028693656 [label="Iter(2)"]
+ n139866027933424 -> n139866028693656
+ n139866027933480 [label=3]
+ n139866027933424 -> n139866027933480
+ n139866027933480 [label=3]
+ n139866027933592 [label="+"]
+ n139866027933424 [label="*"]
+ n139866027933592 -> n139866027933424
+ n139866027933648 [label=2]
+ n139866027933592 -> n139866027933648
+ n139866027933648 [label=2]
+ n139866027930848 [label=Assign]
+ n139866027932080 [label=VectorAccess]
+ n139866027930848 -> n139866027932080
+ n139866027931296 [label=VectorAccess]
+ n139866027930848 -> n139866027931296
+ n139866027933312 [label=VectorAccess]
+ n139866027930848 -> n139866027933312
+ n139866027932528 [label=VectorAccess]
+ n139866027930848 -> n139866027932528
+ n139866027967376 [label=VectorAccess]
+ n139866027930848 -> n139866027967376
+ n139866027966592 [label=VectorAccess]
+ n139866027930848 -> n139866027966592
+ n139866027932080 [label=VectorAccess]
+ n139866027930344 [label=PropertyAccess]
+ n139866027932080 -> n139866027930344
+ n139866027931296 [label=VectorAccess]
+ n139866027930736 [label="+"]
+ n139866027931296 -> n139866027930736
+ n139866027933312 [label=VectorAccess]
+ n139866027930344 [label=PropertyAccess]
+ n139866027933312 -> n139866027930344
+ n139866027932528 [label=VectorAccess]
+ n139866027930736 [label="+"]
+ n139866027932528 -> n139866027930736
+ n139866027967376 [label=VectorAccess]
+ n139866027930344 [label=PropertyAccess]
+ n139866027967376 -> n139866027930344
+ n139866027966592 [label=VectorAccess]
+ n139866027930736 [label="+"]
+ n139866027966592 -> n139866027930736
+ n139866028693544 [label=0]
+ n139866028693320 [label=0]
+}
diff --git a/examples/kernels.pdf b/examples/kernels.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..54c0d45a7732838899d0d081e18c622211358f87
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diff --git a/lift.py b/examples/lift.py
similarity index 100%
rename from lift.py
rename to examples/lift.py
diff --git a/particle.py b/examples/lj_embedded.py
similarity index 65%
rename from particle.py
rename to examples/lj_embedded.py
index 8680d2b..160c608 100644
--- a/particle.py
+++ b/examples/lj_embedded.py
@@ -1,5 +1,5 @@
import pairs
-from ir.layouts import Layout_SoA
+
dt = 0.005
cutoff_radius = 2.5
@@ -13,21 +13,6 @@ mass = psim.add_real_property('mass', 1.0)
position = psim.add_vector_property('position')
velocity = psim.add_vector_property('velocity')
force = psim.add_vector_property('force', vol=True)
-
-#def lj(i, j):
-# sr2 = 1.0 / rsq(i, j)
-# sr6 = sr2 * sr2 * sr2 * sigma6
-# force[i] += delta(i, j) * 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon
-
-#def euler(i):
-# velocity[i] += dt * force[i] / mass[i]
-# position[i] += dt * velocity[i]
-
-# psim.compute(lj)
-# psim.compute(euler)
-
-#grid = psim.grid_3d(0.0, 4.0, 0.0, 4.0, 0.0, 4.0)
-#psim.create_particle_lattice(grid, spacing=[0.82323, 0.82323, 0.82323])
psim.from_file("data/minimd_setup_4x4x4.input", ['mass', 'position', 'velocity'])
psim.create_cell_lists(2.8, 2.8)
psim.create_neighbor_lists()
diff --git a/examples/lj_func.py b/examples/lj_func.py
new file mode 100644
index 0000000..5b2a7d4
--- /dev/null
+++ b/examples/lj_func.py
@@ -0,0 +1,45 @@
+import pairs
+
+
+def delta(i, j):
+ return position[i] - position[j]
+
+
+def rsq(i, j):
+ dp = delta(i, j)
+ return dp.x() * dp.x() + dp.y() * dp.y() + dp.z() * dp.z()
+
+
+def lj(i, j):
+ sr2 = 1.0 / rsq
+ sr6 = sr2 * sr2 * sr2 * sigma6
+ #f = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon
+ #force[i] += delta * f
+ force[i] += delta * 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon
+
+
+def euler(i):
+ velocity[i] += dt * force[i] / mass[i]
+ position[i] += dt * velocity[i]
+
+
+dt = 0.005
+cutoff_radius = 2.5
+skin = 0.3
+sigma = 1.0
+epsilon = 1.0
+sigma6 = sigma ** 6
+
+psim = pairs.simulation("lj_ns")
+psim.add_real_property('mass', 1.0)
+psim.add_vector_property('position')
+psim.add_vector_property('velocity')
+psim.add_vector_property('force', vol=True)
+psim.from_file("data/minimd_setup_4x4x4.input", ['mass', 'position', 'velocity'])
+psim.create_cell_lists(2.8, 2.8)
+psim.create_neighbor_lists()
+psim.periodic(2.8)
+psim.vtk_output("output/test")
+psim.compute(psim, lj, cutoff_radius, 'position', {'sigma6': sigma6, 'epsilon': epsilon})
+psim.compute(psim, euler, symbols={'dt': dt})
+psim.generate()
diff --git a/examples/lj_ns.cpp b/examples/lj_ns.cpp
new file mode 100644
index 0000000..bc536ce
--- /dev/null
+++ b/examples/lj_ns.cpp
@@ -0,0 +1,825 @@
+#include <math.h>
+#include <stdbool.h>
+#include <stdio.h>
+#include <stdlib.h>
+//---
+#include "runtime/pairs.hpp"
+#include "runtime/read_from_file.hpp"
+#include "runtime/vtk.hpp"
+
+using namespace pairs;
+
+int main() {
+ PairsSim *ps = new PairsSim();
+ int particle_capacity = 10000;
+ int nlocal = 0;
+ int nghost = 0;
+ double grid0_d0_min = 0;
+ double grid0_d0_max = 0;
+ double grid0_d1_min = 0;
+ double grid0_d1_max = 0;
+ double grid0_d2_min = 0;
+ double grid0_d2_max = 0;
+ int nstencil = 0;
+ int ncells = 1;
+ int ncells_capacity = 100;
+ int cell_capacity = 20;
+ int neighborlist_capacity = 32;
+ int npbc = 0;
+ int pbc_capacity = 100;
+ int resize = 0;
+ double grid_buffer[6];
+ int dim_cells[3];
+ int *cell_particles = (int *) malloc((sizeof(int) * (ncells_capacity * cell_capacity)));
+ int *cell_sizes = (int *) malloc((sizeof(int) * ncells_capacity));
+ int *stencil = (int *) malloc((sizeof(int) * 27));
+ int *particle_cell = (int *) malloc((sizeof(int) * particle_capacity));
+ int *neighborlists = (int *) malloc((sizeof(int) * (particle_capacity * neighborlist_capacity)));
+ int *numneighs = (int *) malloc((sizeof(int) * particle_capacity));
+ int *pbc_map = (int *) malloc((sizeof(int) * pbc_capacity));
+ int *pbc_mult = (int *) malloc((sizeof(int) * (pbc_capacity * 3)));
+ double *mass = (double *) malloc((sizeof(double) * (particle_capacity + pbc_capacity)));
+ ps->addProperty(Property(0, "mass", mass, Prop_Float));
+ double *position = (double *) malloc((sizeof(double) * ((particle_capacity + pbc_capacity) * 3)));
+ ps->addProperty(Property(1, "position", position, Prop_Vector, AoS, (particle_capacity + pbc_capacity), 3));
+ double *velocity = (double *) malloc((sizeof(double) * ((particle_capacity + pbc_capacity) * 3)));
+ ps->addProperty(Property(2, "velocity", velocity, Prop_Vector, AoS, (particle_capacity + pbc_capacity), 3));
+ double *force = (double *) malloc((sizeof(double) * ((particle_capacity + pbc_capacity) * 3)));
+ ps->addProperty(Property(3, "force", force, Prop_Vector, AoS, (particle_capacity + pbc_capacity), 3));
+ const int prop_list_0[] = {0, 1, 2};
+ nlocal = pairs::read_particle_data(ps, "data/minimd_setup_4x4x4.input", grid_buffer, prop_list_0, 3);
+ const double a0 = grid_buffer[0];
+ grid0_d0_min = a0;
+ const double a1 = grid_buffer[1];
+ grid0_d0_max = a1;
+ const double a2 = grid_buffer[2];
+ grid0_d1_min = a2;
+ const double a3 = grid_buffer[3];
+ grid0_d1_max = a3;
+ const double a4 = grid_buffer[4];
+ grid0_d2_min = a4;
+ const double a5 = grid_buffer[5];
+ grid0_d2_max = a5;
+ fprintf(stdout, "CellListsStencilBuild\n");
+ fflush(stdout);
+ const double e462 = grid0_d0_max - grid0_d0_min;
+ const double e463 = e462 / 2.8;
+ const int e464 = ceil(e463) + 2;
+ dim_cells[0] = e464;
+ const double e466 = grid0_d1_max - grid0_d1_min;
+ const double e467 = e466 / 2.8;
+ const int e468 = ceil(e467) + 2;
+ dim_cells[1] = e468;
+ const int a54 = dim_cells[0];
+ const int a56 = dim_cells[1];
+ const int e469 = a54 * a56;
+ const double e470 = grid0_d2_max - grid0_d2_min;
+ const double e471 = e470 / 2.8;
+ const int e472 = ceil(e471) + 2;
+ dim_cells[2] = e472;
+ const int a58 = dim_cells[2];
+ const int e473 = e469 * a58;
+ ncells = e473;
+ resize = 1;
+ while((resize > 0)) {
+ resize = 0;
+ const bool e475 = ncells >= ncells_capacity;
+ if(e475) {
+ resize = ncells;
+ }
+ const bool e476 = resize > 0;
+ if(e476) {
+ fprintf(stdout, "Resize ncells_capacity\n");
+ fflush(stdout);
+ const int e477 = resize * 2;
+ ncells_capacity = e477;
+ cell_particles = (int *) realloc(cell_particles, (sizeof(int) * (ncells_capacity * cell_capacity)));
+ cell_sizes = (int *) realloc(cell_sizes, (sizeof(int) * ncells_capacity));
+ }
+ }
+ nstencil = 0;
+ for(int i15 = -1; i15 < 2; i15++) {
+ const int a59 = dim_cells[0];
+ const int e481 = i15 * a59;
+ for(int i16 = -1; i16 < 2; i16++) {
+ const int e482 = e481 + i16;
+ const int a60 = dim_cells[1];
+ const int e483 = e482 * a60;
+ for(int i17 = -1; i17 < 2; i17++) {
+ const int e484 = e483 + i17;
+ stencil[nstencil] = e484;
+ const int e485 = nstencil + 1;
+ nstencil = e485;
+ }
+ }
+ }
+ const int e486 = nlocal + npbc;
+ pairs::vtk_write_data(ps, "output/test_local", 0, nlocal, 0);
+ pairs::vtk_write_data(ps, "output/test_pbc", nlocal, e486, 0);
+ for(int i14 = 0; i14 < 101; i14++) {
+ const int e452 = i14 % 20;
+ const bool e453 = e452 == 0;
+ if(e453) {
+ fprintf(stdout, "EnforcePBC\n");
+ fflush(stdout);
+ const double e115 = grid0_d0_max - grid0_d0_min;
+ const double e122 = grid0_d0_max - grid0_d0_min;
+ const double e129 = grid0_d1_max - grid0_d1_min;
+ const double e136 = grid0_d1_max - grid0_d1_min;
+ const double e143 = grid0_d2_max - grid0_d2_min;
+ const double e150 = grid0_d2_max - grid0_d2_min;
+ for(int i3 = 0; i3 < nlocal; i3++) {
+ const int e110 = i3 * 3;
+ const double p8_0 = position[e110];
+ const bool e112 = p8_0 < grid0_d0_min;
+ if(e112) {
+ const int e113 = i3 * 3;
+ const double p9_0 = position[e113];
+ const double e116 = p9_0 + e115;
+ position[e113] = e116;
+ }
+ const int e117 = i3 * 3;
+ const double p10_0 = position[e117];
+ const bool e119 = p10_0 > grid0_d0_max;
+ if(e119) {
+ const int e120 = i3 * 3;
+ const double p11_0 = position[e120];
+ const double e123 = p11_0 - e122;
+ position[e120] = e123;
+ }
+ const int e124 = i3 * 3;
+ const int e125 = e124 + 1;
+ const double p12_1 = position[e125];
+ const bool e126 = p12_1 < grid0_d1_min;
+ if(e126) {
+ const int e127 = i3 * 3;
+ const int e128 = e127 + 1;
+ const double p13_1 = position[e128];
+ const double e130 = p13_1 + e129;
+ position[e128] = e130;
+ }
+ const int e131 = i3 * 3;
+ const int e132 = e131 + 1;
+ const double p14_1 = position[e132];
+ const bool e133 = p14_1 > grid0_d1_max;
+ if(e133) {
+ const int e134 = i3 * 3;
+ const int e135 = e134 + 1;
+ const double p15_1 = position[e135];
+ const double e137 = p15_1 - e136;
+ position[e135] = e137;
+ }
+ const int e138 = i3 * 3;
+ const int e139 = e138 + 2;
+ const double p16_2 = position[e139];
+ const bool e140 = p16_2 < grid0_d2_min;
+ if(e140) {
+ const int e141 = i3 * 3;
+ const int e142 = e141 + 2;
+ const double p17_2 = position[e142];
+ const double e144 = p17_2 + e143;
+ position[e142] = e144;
+ }
+ const int e145 = i3 * 3;
+ const int e146 = e145 + 2;
+ const double p18_2 = position[e146];
+ const bool e147 = p18_2 > grid0_d2_max;
+ if(e147) {
+ const int e148 = i3 * 3;
+ const int e149 = e148 + 2;
+ const double p19_2 = position[e149];
+ const double e151 = p19_2 - e150;
+ position[e149] = e151;
+ }
+ }
+ }
+ const int e454 = i14 % 20;
+ const bool e455 = e454 == 0;
+ if(e455) {
+ fprintf(stdout, "SetupPBC\n");
+ fflush(stdout);
+ resize = 1;
+ while((resize > 0)) {
+ resize = 0;
+ npbc = 0;
+ const int e153 = nlocal + npbc;
+ const double e157 = grid0_d0_min + 2.8;
+ const double e168 = grid0_d0_max - grid0_d0_min;
+ const double e185 = grid0_d0_max - 2.8;
+ const double e196 = grid0_d0_max - grid0_d0_min;
+ for(int i4 = 0; i4 < e153; i4++) {
+ const int e154 = nlocal + npbc;
+ const int e155 = i4 * 3;
+ const double p20_0 = position[e155];
+ const bool e158 = p20_0 < e157;
+ if(e158) {
+ const bool e159 = npbc >= pbc_capacity;
+ if(e159) {
+ const bool e160 = resize > npbc;
+ resize = (e160) ? ((resize + 1)) : (npbc);
+ } else {
+ pbc_map[npbc] = i4;
+ const int e162 = npbc * 3;
+ pbc_mult[e162] = 1;
+ const int e164 = e154 * 3;
+ const double p21_0 = position[e164];
+ const int e166 = i4 * 3;
+ const double p22_0 = position[e166];
+ const double e169 = p22_0 + e168;
+ position[e164] = e169;
+ const int e170 = npbc * 3;
+ const int e171 = e170 + 1;
+ pbc_mult[e171] = 0;
+ const int e172 = e154 * 3;
+ const int e173 = e172 + 1;
+ const double p23_1 = position[e173];
+ const int e174 = i4 * 3;
+ const int e175 = e174 + 1;
+ const double p24_1 = position[e175];
+ position[e173] = p24_1;
+ const int e176 = npbc * 3;
+ const int e177 = e176 + 2;
+ pbc_mult[e177] = 0;
+ const int e178 = e154 * 3;
+ const int e179 = e178 + 2;
+ const double p25_2 = position[e179];
+ const int e180 = i4 * 3;
+ const int e181 = e180 + 2;
+ const double p26_2 = position[e181];
+ position[e179] = p26_2;
+ const int e182 = npbc + 1;
+ npbc = e182;
+ }
+ }
+ const int e183 = i4 * 3;
+ const double p27_0 = position[e183];
+ const bool e186 = p27_0 > e185;
+ if(e186) {
+ const bool e187 = npbc >= pbc_capacity;
+ if(e187) {
+ const bool e188 = resize > npbc;
+ resize = (e188) ? ((resize + 1)) : (npbc);
+ } else {
+ pbc_map[npbc] = i4;
+ const int e190 = npbc * 3;
+ pbc_mult[e190] = -1;
+ const int e192 = e154 * 3;
+ const double p28_0 = position[e192];
+ const int e194 = i4 * 3;
+ const double p29_0 = position[e194];
+ const double e197 = p29_0 - e196;
+ position[e192] = e197;
+ const int e198 = npbc * 3;
+ const int e199 = e198 + 1;
+ pbc_mult[e199] = 0;
+ const int e200 = e154 * 3;
+ const int e201 = e200 + 1;
+ const double p30_1 = position[e201];
+ const int e202 = i4 * 3;
+ const int e203 = e202 + 1;
+ const double p31_1 = position[e203];
+ position[e201] = p31_1;
+ const int e204 = npbc * 3;
+ const int e205 = e204 + 2;
+ pbc_mult[e205] = 0;
+ const int e206 = e154 * 3;
+ const int e207 = e206 + 2;
+ const double p32_2 = position[e207];
+ const int e208 = i4 * 3;
+ const int e209 = e208 + 2;
+ const double p33_2 = position[e209];
+ position[e207] = p33_2;
+ const int e210 = npbc + 1;
+ npbc = e210;
+ }
+ }
+ }
+ const int e211 = nlocal + npbc;
+ const double e215 = grid0_d1_min + 2.8;
+ const double e226 = grid0_d1_max - grid0_d1_min;
+ const double e243 = grid0_d1_max - 2.8;
+ const double e254 = grid0_d1_max - grid0_d1_min;
+ for(int i5 = 0; i5 < e211; i5++) {
+ const int e212 = nlocal + npbc;
+ const int e213 = i5 * 3;
+ const int e214 = e213 + 1;
+ const double p34_1 = position[e214];
+ const bool e216 = p34_1 < e215;
+ if(e216) {
+ const bool e217 = npbc >= pbc_capacity;
+ if(e217) {
+ const bool e218 = resize > npbc;
+ resize = (e218) ? ((resize + 1)) : (npbc);
+ } else {
+ pbc_map[npbc] = i5;
+ const int e220 = npbc * 3;
+ const int e221 = e220 + 1;
+ pbc_mult[e221] = 1;
+ const int e222 = e212 * 3;
+ const int e223 = e222 + 1;
+ const double p35_1 = position[e223];
+ const int e224 = i5 * 3;
+ const int e225 = e224 + 1;
+ const double p36_1 = position[e225];
+ const double e227 = p36_1 + e226;
+ position[e223] = e227;
+ const int e228 = npbc * 3;
+ pbc_mult[e228] = 0;
+ const int e230 = e212 * 3;
+ const double p37_0 = position[e230];
+ const int e232 = i5 * 3;
+ const double p38_0 = position[e232];
+ position[e230] = p38_0;
+ const int e234 = npbc * 3;
+ const int e235 = e234 + 2;
+ pbc_mult[e235] = 0;
+ const int e236 = e212 * 3;
+ const int e237 = e236 + 2;
+ const double p39_2 = position[e237];
+ const int e238 = i5 * 3;
+ const int e239 = e238 + 2;
+ const double p40_2 = position[e239];
+ position[e237] = p40_2;
+ const int e240 = npbc + 1;
+ npbc = e240;
+ }
+ }
+ const int e241 = i5 * 3;
+ const int e242 = e241 + 1;
+ const double p41_1 = position[e242];
+ const bool e244 = p41_1 > e243;
+ if(e244) {
+ const bool e245 = npbc >= pbc_capacity;
+ if(e245) {
+ const bool e246 = resize > npbc;
+ resize = (e246) ? ((resize + 1)) : (npbc);
+ } else {
+ pbc_map[npbc] = i5;
+ const int e248 = npbc * 3;
+ const int e249 = e248 + 1;
+ pbc_mult[e249] = -1;
+ const int e250 = e212 * 3;
+ const int e251 = e250 + 1;
+ const double p42_1 = position[e251];
+ const int e252 = i5 * 3;
+ const int e253 = e252 + 1;
+ const double p43_1 = position[e253];
+ const double e255 = p43_1 - e254;
+ position[e251] = e255;
+ const int e256 = npbc * 3;
+ pbc_mult[e256] = 0;
+ const int e258 = e212 * 3;
+ const double p44_0 = position[e258];
+ const int e260 = i5 * 3;
+ const double p45_0 = position[e260];
+ position[e258] = p45_0;
+ const int e262 = npbc * 3;
+ const int e263 = e262 + 2;
+ pbc_mult[e263] = 0;
+ const int e264 = e212 * 3;
+ const int e265 = e264 + 2;
+ const double p46_2 = position[e265];
+ const int e266 = i5 * 3;
+ const int e267 = e266 + 2;
+ const double p47_2 = position[e267];
+ position[e265] = p47_2;
+ const int e268 = npbc + 1;
+ npbc = e268;
+ }
+ }
+ }
+ const int e269 = nlocal + npbc;
+ const double e273 = grid0_d2_min + 2.8;
+ const double e284 = grid0_d2_max - grid0_d2_min;
+ const double e301 = grid0_d2_max - 2.8;
+ const double e312 = grid0_d2_max - grid0_d2_min;
+ for(int i6 = 0; i6 < e269; i6++) {
+ const int e270 = nlocal + npbc;
+ const int e271 = i6 * 3;
+ const int e272 = e271 + 2;
+ const double p48_2 = position[e272];
+ const bool e274 = p48_2 < e273;
+ if(e274) {
+ const bool e275 = npbc >= pbc_capacity;
+ if(e275) {
+ const bool e276 = resize > npbc;
+ resize = (e276) ? ((resize + 1)) : (npbc);
+ } else {
+ pbc_map[npbc] = i6;
+ const int e278 = npbc * 3;
+ const int e279 = e278 + 2;
+ pbc_mult[e279] = 1;
+ const int e280 = e270 * 3;
+ const int e281 = e280 + 2;
+ const double p49_2 = position[e281];
+ const int e282 = i6 * 3;
+ const int e283 = e282 + 2;
+ const double p50_2 = position[e283];
+ const double e285 = p50_2 + e284;
+ position[e281] = e285;
+ const int e286 = npbc * 3;
+ pbc_mult[e286] = 0;
+ const int e288 = e270 * 3;
+ const double p51_0 = position[e288];
+ const int e290 = i6 * 3;
+ const double p52_0 = position[e290];
+ position[e288] = p52_0;
+ const int e292 = npbc * 3;
+ const int e293 = e292 + 1;
+ pbc_mult[e293] = 0;
+ const int e294 = e270 * 3;
+ const int e295 = e294 + 1;
+ const double p53_1 = position[e295];
+ const int e296 = i6 * 3;
+ const int e297 = e296 + 1;
+ const double p54_1 = position[e297];
+ position[e295] = p54_1;
+ const int e298 = npbc + 1;
+ npbc = e298;
+ }
+ }
+ const int e299 = i6 * 3;
+ const int e300 = e299 + 2;
+ const double p55_2 = position[e300];
+ const bool e302 = p55_2 > e301;
+ if(e302) {
+ const bool e303 = npbc >= pbc_capacity;
+ if(e303) {
+ const bool e304 = resize > npbc;
+ resize = (e304) ? ((resize + 1)) : (npbc);
+ } else {
+ pbc_map[npbc] = i6;
+ const int e306 = npbc * 3;
+ const int e307 = e306 + 2;
+ pbc_mult[e307] = -1;
+ const int e308 = e270 * 3;
+ const int e309 = e308 + 2;
+ const double p56_2 = position[e309];
+ const int e310 = i6 * 3;
+ const int e311 = e310 + 2;
+ const double p57_2 = position[e311];
+ const double e313 = p57_2 - e312;
+ position[e309] = e313;
+ const int e314 = npbc * 3;
+ pbc_mult[e314] = 0;
+ const int e316 = e270 * 3;
+ const double p58_0 = position[e316];
+ const int e318 = i6 * 3;
+ const double p59_0 = position[e318];
+ position[e316] = p59_0;
+ const int e320 = npbc * 3;
+ const int e321 = e320 + 1;
+ pbc_mult[e321] = 0;
+ const int e322 = e270 * 3;
+ const int e323 = e322 + 1;
+ const double p60_1 = position[e323];
+ const int e324 = i6 * 3;
+ const int e325 = e324 + 1;
+ const double p61_1 = position[e325];
+ position[e323] = p61_1;
+ const int e326 = npbc + 1;
+ npbc = e326;
+ }
+ }
+ }
+ const bool e327 = resize > 0;
+ if(e327) {
+ fprintf(stdout, "Resize pbc_capacity\n");
+ fflush(stdout);
+ const int e328 = resize * 2;
+ pbc_capacity = e328;
+ pbc_map = (int *) realloc(pbc_map, (sizeof(int) * pbc_capacity));
+ pbc_mult = (int *) realloc(pbc_mult, (sizeof(int) * (pbc_capacity * 3)));
+ mass = (double *) realloc(mass, (sizeof(double) * (particle_capacity + pbc_capacity)));
+ ps->updateProperty(0, mass);
+ position = (double *) realloc(position, (sizeof(double) * ((particle_capacity + pbc_capacity) * 3)));
+ ps->updateProperty(1, position, (particle_capacity + pbc_capacity), 3);
+ velocity = (double *) realloc(velocity, (sizeof(double) * ((particle_capacity + pbc_capacity) * 3)));
+ ps->updateProperty(2, velocity, (particle_capacity + pbc_capacity), 3);
+ force = (double *) realloc(force, (sizeof(double) * ((particle_capacity + pbc_capacity) * 3)));
+ ps->updateProperty(3, force, (particle_capacity + pbc_capacity), 3);
+ }
+ }
+ } else {
+ fprintf(stdout, "UpdatePBC\n");
+ fflush(stdout);
+ const double e348 = grid0_d0_max - grid0_d0_min;
+ const double e358 = grid0_d1_max - grid0_d1_min;
+ const double e368 = grid0_d2_max - grid0_d2_min;
+ for(int i7 = 0; i7 < npbc; i7++) {
+ const int e341 = nlocal + i7;
+ const int e342 = e341 * 3;
+ const double p62_0 = position[e342];
+ const int a32 = pbc_map[i7];
+ const int e344 = a32 * 3;
+ const double p63_0 = position[e344];
+ const int e346 = i7 * 3;
+ const int a33 = pbc_mult[e346];
+ const double e349 = a33 * e348;
+ const double e350 = p63_0 + e349;
+ position[e342] = e350;
+ const int e351 = nlocal + i7;
+ const int e352 = e351 * 3;
+ const int e353 = e352 + 1;
+ const double p64_1 = position[e353];
+ const int a34 = pbc_map[i7];
+ const int e354 = a34 * 3;
+ const int e355 = e354 + 1;
+ const double p65_1 = position[e355];
+ const int e356 = i7 * 3;
+ const int e357 = e356 + 1;
+ const int a35 = pbc_mult[e357];
+ const double e359 = a35 * e358;
+ const double e360 = p65_1 + e359;
+ position[e353] = e360;
+ const int e361 = nlocal + i7;
+ const int e362 = e361 * 3;
+ const int e363 = e362 + 2;
+ const double p66_2 = position[e363];
+ const int a36 = pbc_map[i7];
+ const int e364 = a36 * 3;
+ const int e365 = e364 + 2;
+ const double p67_2 = position[e365];
+ const int e366 = i7 * 3;
+ const int e367 = e366 + 2;
+ const int a37 = pbc_mult[e367];
+ const double e369 = a37 * e368;
+ const double e370 = p67_2 + e369;
+ position[e363] = e370;
+ }
+ }
+ const int e456 = i14 % 20;
+ const bool e457 = e456 == 0;
+ if(e457) {
+ fprintf(stdout, "CellListsBuild\n");
+ fflush(stdout);
+ resize = 1;
+ while((resize > 0)) {
+ resize = 0;
+ for(int i8 = 0; i8 < ncells; i8++) {
+ cell_sizes[i8] = 0;
+ }
+ const int e511 = nlocal + npbc;
+ for(int i9 = 0; i9 < e511; i9++) {
+ const int e372 = i9 * 3;
+ const double p68_0 = position[e372];
+ const double e374 = p68_0 - grid0_d0_min;
+ const double e375 = e374 / 2.8;
+ const int e376 = i9 * 3;
+ const int e377 = e376 + 1;
+ const double p69_1 = position[e377];
+ const double e378 = p69_1 - grid0_d1_min;
+ const double e379 = e378 / 2.8;
+ const int e380 = i9 * 3;
+ const int e381 = e380 + 2;
+ const double p70_2 = position[e381];
+ const double e382 = p70_2 - grid0_d2_min;
+ const double e383 = e382 / 2.8;
+ const int a39 = dim_cells[1];
+ const int e384 = (int)(e375) * a39;
+ const int e385 = e384 + (int)(e379);
+ const int a40 = dim_cells[2];
+ const int e386 = e385 * a40;
+ const int e387 = e386 + (int)(e383);
+ const bool e388 = e387 >= 0;
+ const bool e389 = e387 <= ncells;
+ const bool e390 = e388 && e389;
+ if(e390) {
+ const int a41 = cell_sizes[e387];
+ const bool e391 = a41 >= cell_capacity;
+ if(e391) {
+ resize = a41;
+ } else {
+ const int e392 = e387 * cell_capacity;
+ const int e393 = e392 + a41;
+ cell_particles[e393] = i9;
+ particle_cell[i9] = e387;
+ }
+ const int e394 = a41 + 1;
+ cell_sizes[e387] = e394;
+ }
+ }
+ const bool e395 = resize > 0;
+ if(e395) {
+ fprintf(stdout, "Resize cell_capacity\n");
+ fflush(stdout);
+ const int e396 = resize * 2;
+ cell_capacity = e396;
+ cell_particles = (int *) realloc(cell_particles, (sizeof(int) * (ncells_capacity * cell_capacity)));
+ }
+ }
+ }
+ const int e458 = i14 % 20;
+ const bool e459 = e458 == 0;
+ if(e459) {
+ fprintf(stdout, "NeighborListsBuild\n");
+ fflush(stdout);
+ resize = 1;
+ while((resize > 0)) {
+ resize = 0;
+ for(int i10 = 0; i10 < nlocal; i10++) {
+ numneighs[i10] = 0;
+ for(int i11 = 0; i11 < nstencil; i11++) {
+ const int a46 = particle_cell[i10];
+ const int a47 = stencil[i11];
+ const int e400 = a46 + a47;
+ const bool e401 = e400 >= 0;
+ const bool e402 = e400 <= ncells;
+ const bool e403 = e401 && e402;
+ if(e403) {
+ const int e404 = e400 * cell_capacity;
+ const int e412 = i10 * 3;
+ const double p71_0 = position[e412];
+ const int e421 = i10 * 3;
+ const int e422 = e421 + 1;
+ const double p71_1 = position[e422];
+ const int e431 = i10 * 3;
+ const int e432 = e431 + 2;
+ const double p71_2 = position[e432];
+ const int e439 = i10 * neighborlist_capacity;
+ const int a48 = cell_sizes[e400];
+ for(int i12 = 0; i12 < a48; i12++) {
+ const int e405 = e404 + i12;
+ const int a49 = cell_particles[e405];
+ const bool e406 = a49 != i10;
+ if(e406) {
+ const int e414 = a49 * 3;
+ const double p72_0 = position[e414];
+ const int e423 = a49 * 3;
+ const int e424 = e423 + 1;
+ const double p72_1 = position[e424];
+ const int e433 = a49 * 3;
+ const int e434 = e433 + 2;
+ const double p72_2 = position[e434];
+ const double e407_0 = p71_0 - p72_0;
+ const double e407_1 = p71_1 - p72_1;
+ const double e407_2 = p71_2 - p72_2;
+ const double e416 = e407_0 * e407_0;
+ const double e425 = e407_1 * e407_1;
+ const double e426 = e416 + e425;
+ const double e435 = e407_2 * e407_2;
+ const double e436 = e426 + e435;
+ const bool e437 = e436 < 2.8;
+ if(e437) {
+ const int a50 = numneighs[i10];
+ const bool e438 = a50 >= neighborlist_capacity;
+ if(e438) {
+ resize = a50;
+ } else {
+ const int e440 = e439 + a50;
+ neighborlists[e440] = a49;
+ const int e441 = a50 + 1;
+ numneighs[i10] = e441;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ const bool e442 = resize > 0;
+ if(e442) {
+ fprintf(stdout, "Resize neighborlist_capacity\n");
+ fflush(stdout);
+ const int e443 = resize * 2;
+ neighborlist_capacity = e443;
+ neighborlists = (int *) realloc(neighborlists, (sizeof(int) * (particle_capacity * neighborlist_capacity)));
+ }
+ }
+ }
+ fprintf(stdout, "PropertiesResetVolatile\n");
+ fflush(stdout);
+ for(int i13 = 0; i13 < nlocal; i13++) {
+ const int e446 = i13 * 3;
+ const double p73_0 = force[e446];
+ const int e448 = i13 * 3;
+ const int e449 = e448 + 1;
+ const double p73_1 = force[e449];
+ const int e450 = i13 * 3;
+ const int e451 = e450 + 2;
+ const double p73_2 = force[e451];
+ force[e446] = 0.0;
+ force[e449] = 0.0;
+ force[e451] = 0.0;
+ }
+ for(int i0 = 0; i0 < nlocal; i0++) {
+ const int e1 = i0 * neighborlist_capacity;
+ const int e47 = i0 * 3;
+ const double p0_0 = position[e47];
+ const int e55 = i0 * 3;
+ const int e56 = e55 + 1;
+ const double p0_1 = position[e56];
+ const int e63 = i0 * 3;
+ const int e64 = e63 + 2;
+ const double p0_2 = position[e64];
+ const int e51 = i0 * 3;
+ const int e59 = i0 * 3;
+ const int e60 = e59 + 1;
+ const int e67 = i0 * 3;
+ const int e68 = e67 + 2;
+ const int a6 = numneighs[i0];
+ for(int i1 = 0; i1 < a6; i1++) {
+ const int e2 = e1 + i1;
+ const int a7 = neighborlists[e2];
+ const int e49 = a7 * 3;
+ const double p1_0 = position[e49];
+ const int e57 = a7 * 3;
+ const int e58 = e57 + 1;
+ const double p1_1 = position[e58];
+ const int e65 = a7 * 3;
+ const int e66 = e65 + 2;
+ const double p1_2 = position[e66];
+ const double e3_0 = p0_0 - p1_0;
+ const double e3_1 = p0_1 - p1_1;
+ const double e3_2 = p0_2 - p1_2;
+ const double e12 = e3_0 * e3_0;
+ const double e21 = e3_1 * e3_1;
+ const double e22 = e12 + e21;
+ const double e31 = e3_2 * e3_2;
+ const double e32 = e22 + e31;
+ const bool e33 = e32 < 2.5;
+ if(e33) {
+ const double e34 = 1.0 / e32;
+ const double e35 = e34 * e34;
+ const double e36 = e35 * e34;
+ const double p2_0 = force[e51];
+ const double p2_1 = force[e60];
+ const double p2_2 = force[e68];
+ const double e40 = e36 - 0.5;
+ const double e507 = 48.0 * e36;
+ const double e508 = e507 * e40;
+ const double e509 = e508 * e34;
+ const double e43_0 = e3_0 * e509;
+ const double e43_1 = e3_1 * e509;
+ const double e43_2 = e3_2 * e509;
+ const double e44_0 = p2_0 + e43_0;
+ const double e44_1 = p2_1 + e43_1;
+ const double e44_2 = p2_2 + e43_2;
+ force[e51] = e44_0;
+ force[e60] = e44_1;
+ force[e68] = e44_2;
+ }
+ }
+ }
+ for(int i2 = 0; i2 < nlocal; i2++) {
+ const int e76 = i2 * 3;
+ const double p3_0 = velocity[e76];
+ const int e82 = i2 * 3;
+ const int e83 = e82 + 1;
+ const double p3_1 = velocity[e83];
+ const int e88 = i2 * 3;
+ const int e89 = e88 + 2;
+ const double p3_2 = velocity[e89];
+ const int e74 = i2 * 3;
+ const double p4_0 = force[e74];
+ const int e80 = i2 * 3;
+ const int e81 = e80 + 1;
+ const double p4_1 = force[e81];
+ const int e86 = i2 * 3;
+ const int e87 = e86 + 2;
+ const double p4_2 = force[e87];
+ const double e69_0 = 0.005 * p4_0;
+ const double e69_1 = 0.005 * p4_1;
+ const double e69_2 = 0.005 * p4_2;
+ const double p5 = mass[i2];
+ const double e70_0 = e69_0 / p5;
+ const double e70_1 = e69_1 / p5;
+ const double e70_2 = e69_2 / p5;
+ const double e71_0 = p3_0 + e70_0;
+ const double e71_1 = p3_1 + e70_1;
+ const double e71_2 = p3_2 + e70_2;
+ velocity[e76] = e71_0;
+ velocity[e83] = e71_1;
+ velocity[e89] = e71_2;
+ const int e96 = i2 * 3;
+ const double p6_0 = position[e96];
+ const int e102 = i2 * 3;
+ const int e103 = e102 + 1;
+ const double p6_1 = position[e103];
+ const int e108 = i2 * 3;
+ const int e109 = e108 + 2;
+ const double p6_2 = position[e109];
+ const int e94 = i2 * 3;
+ const double p7_0 = velocity[e94];
+ const int e100 = i2 * 3;
+ const int e101 = e100 + 1;
+ const double p7_1 = velocity[e101];
+ const int e106 = i2 * 3;
+ const int e107 = e106 + 2;
+ const double p7_2 = velocity[e107];
+ const double e90_0 = 0.005 * p7_0;
+ const double e90_1 = 0.005 * p7_1;
+ const double e90_2 = 0.005 * p7_2;
+ const double e91_0 = p6_0 + e90_0;
+ const double e91_1 = p6_1 + e90_1;
+ const double e91_2 = p6_2 + e90_2;
+ position[e96] = e91_0;
+ position[e103] = e91_1;
+ position[e109] = e91_2;
+ }
+ const int e461 = nlocal + npbc;
+ const int e460 = i14 + 1;
+ pairs::vtk_write_data(ps, "output/test_local", 0, nlocal, e460);
+ pairs::vtk_write_data(ps, "output/test_pbc", nlocal, e461, e460);
+ }
+}
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..374b58c
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,6 @@
+[build-system]
+requires = [
+ "setuptools>=42",
+ "wheel"
+]
+build-backend = "setuptools.build_meta"
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..c9a1f5f
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,46 @@
+import setuptools
+
+
+def readme():
+ with open('README.md') as f:
+ return f.read()
+
+
+modules = [
+ 'code_gen',
+ 'coupling',
+ 'graph',
+ 'ir',
+ 'mapping',
+ 'runtime',
+ 'sim',
+ 'transformations',
+]
+
+setuptools.setup(name='pairs',
+ description="A code generator for particle simulations",
+ version="0.0.1",
+ long_description=readme(),
+ long_description_content_type="text/markdown",
+ author="Rafael Ravedutti Lucio Machado",
+ license='MIT',
+ author_email="rafael.r.ravedutti@fau.de",
+ url="https://github.com/rafaelravedutti/pairs",
+ install_requires=[],
+ packages=['pairs'] + [f"pairs.{mod}" for mod in modules],
+ package_dir={'pairs': 'src/pairs'},
+ package_data={'pairs.runtime': ['runtime/*.hpp']},
+ classifiers=[
+ "Programming Language :: Python :: 3",
+ "License :: OSI Approved :: MIT License",
+ "Operating System :: OS Independent",
+ ],
+ project_urls={
+ "Bug Tracker": "https://github.com/rafaelravedutti/pairs",
+ "Documentation": "https://github.com/rafaelravedutti/pairs",
+ "Source Code": "https://github.com/rafaelravedutti/pairs",
+ },
+ extras_require={},
+ tests_require=[],
+ python_requires=">=3.6",
+)
diff --git a/code_gen/__init__.py b/src/__init__.py
similarity index 100%
rename from code_gen/__init__.py
rename to src/__init__.py
diff --git a/pairs.py b/src/pairs/__init__.py
similarity index 53%
rename from pairs.py
rename to src/pairs/__init__.py
index d816433..5a71e58 100644
--- a/pairs.py
+++ b/src/pairs/__init__.py
@@ -1,5 +1,5 @@
-from code_gen.cgen import CGen
-from sim.particle_simulation import ParticleSimulation
+from pairs.code_gen.cgen import CGen
+from pairs.sim.particle_simulation import ParticleSimulation
def simulation(ref, dims=3, timesteps=100):
diff --git a/coupling/__init__.py b/src/pairs/code_gen/__init__.py
similarity index 100%
rename from coupling/__init__.py
rename to src/pairs/code_gen/__init__.py
diff --git a/code_gen/cgen.py b/src/pairs/code_gen/cgen.py
similarity index 93%
rename from code_gen/cgen.py
rename to src/pairs/code_gen/cgen.py
index 93ea927..219e9e9 100644
--- a/code_gen/cgen.py
+++ b/src/pairs/code_gen/cgen.py
@@ -1,23 +1,23 @@
-from ir.assign import Assign
-from ir.arrays import Array, ArrayAccess, ArrayDecl
-from ir.block import Block
-from ir.branches import Branch
-from ir.cast import Cast
-from ir.bin_op import BinOp, Decl, VectorAccess
-from ir.data_types import Type_Int, Type_Float, Type_String, Type_Vector
-from ir.functions import Call
-from ir.layouts import Layout_AoS, Layout_SoA, Layout_Invalid
-from ir.lit import Lit
-from ir.loops import For, Iter, ParticleFor, While
-from ir.math import Ceil, Sqrt
-from ir.memory import Malloc, Realloc
-from ir.properties import Property, PropertyAccess, PropertyList, RegisterProperty, UpdateProperty
-from ir.select import Select
-from ir.sizeof import Sizeof
-from ir.utils import Print
-from ir.variables import Var, VarDecl
-from sim.timestep import Timestep
-from code_gen.printer import Printer
+from pairs.ir.assign import Assign
+from pairs.ir.arrays import Array, ArrayAccess, ArrayDecl
+from pairs.ir.block import Block
+from pairs.ir.branches import Branch
+from pairs.ir.cast import Cast
+from pairs.ir.bin_op import BinOp, Decl, VectorAccess
+from pairs.ir.data_types import Type_Int, Type_Float, Type_String, Type_Vector
+from pairs.ir.functions import Call
+from pairs.ir.layouts import Layout_AoS, Layout_SoA, Layout_Invalid
+from pairs.ir.lit import Lit
+from pairs.ir.loops import For, Iter, ParticleFor, While
+from pairs.ir.math import Ceil, Sqrt
+from pairs.ir.memory import Malloc, Realloc
+from pairs.ir.properties import Property, PropertyAccess, PropertyList, RegisterProperty, UpdateProperty
+from pairs.ir.select import Select
+from pairs.ir.sizeof import Sizeof
+from pairs.ir.utils import Print
+from pairs.ir.variables import Var, VarDecl
+from pairs.sim.timestep import Timestep
+from pairs.code_gen.printer import Printer
class CGen:
diff --git a/code_gen/printer.py b/src/pairs/code_gen/printer.py
similarity index 100%
rename from code_gen/printer.py
rename to src/pairs/code_gen/printer.py
diff --git a/ir/__init__.py b/src/pairs/coupling/__init__.py
similarity index 100%
rename from ir/__init__.py
rename to src/pairs/coupling/__init__.py
diff --git a/coupling/parse_cpp.py b/src/pairs/coupling/parse_cpp.py
similarity index 97%
rename from coupling/parse_cpp.py
rename to src/pairs/coupling/parse_cpp.py
index 726475e..8c94702 100644
--- a/coupling/parse_cpp.py
+++ b/src/pairs/coupling/parse_cpp.py
@@ -1,10 +1,10 @@
-from ast.block import Block
-from ast.branches import Branch
-from ast.data_types import Type_Float, Type_Vector
-from ast.math import Sqrt
-from ast.select import Select
import clang.cindex
from clang.cindex import CursorKind as kind
+from pairs.ast.block import Block
+from pairs.ast.branches import Branch
+from pairs.ast.data_types import Type_Float, Type_Vector
+from pairs.ast.math import Sqrt
+from pairs.ast.select import Select
def print_tree(node, indent=0):
diff --git a/sim/__init__.py b/src/pairs/graph/__init__.py
similarity index 100%
rename from sim/__init__.py
rename to src/pairs/graph/__init__.py
diff --git a/graph/graphviz.py b/src/pairs/graph/graphviz.py
similarity index 86%
rename from graph/graphviz.py
rename to src/pairs/graph/graphviz.py
index e078b42..535abe4 100644
--- a/graph/graphviz.py
+++ b/src/pairs/graph/graphviz.py
@@ -1,11 +1,11 @@
-from ir.arrays import Array
-from ir.bin_op import BinOp, Decl
-from ir.lit import Lit
-from ir.loops import Iter
-from ir.properties import Property
-from ir.variables import Var
-from ir.visitor import Visitor
from graphviz import Digraph
+from pairs.ir.arrays import Array
+from pairs.ir.bin_op import BinOp, Decl
+from pairs.ir.lit import Lit
+from pairs.ir.loops import Iter
+from pairs.ir.properties import Property
+from pairs.ir.variables import Var
+from pairs.ir.visitor import Visitor
class ASTGraph:
diff --git a/ir/operators.py b/src/pairs/ir/__init__.py
similarity index 100%
rename from ir/operators.py
rename to src/pairs/ir/__init__.py
diff --git a/ir/arrays.py b/src/pairs/ir/arrays.py
similarity index 94%
rename from ir/arrays.py
rename to src/pairs/ir/arrays.py
index a49e39a..49aeb88 100644
--- a/ir/arrays.py
+++ b/src/pairs/ir/arrays.py
@@ -1,12 +1,12 @@
-from ir.assign import Assign
-from ir.ast_node import ASTNode
-from ir.bin_op import BinOp, ASTTerm
-from ir.data_types import Type_Array
-from ir.layouts import Layout_AoS, Layout_SoA
-from ir.lit import as_lit_ast
-from ir.memory import Realloc
-from ir.variables import Var
from functools import reduce
+from pairs.ir.assign import Assign
+from pairs.ir.ast_node import ASTNode
+from pairs.ir.bin_op import BinOp, ASTTerm
+from pairs.ir.data_types import Type_Array
+from pairs.ir.layouts import Layout_AoS, Layout_SoA
+from pairs.ir.lit import as_lit_ast
+from pairs.ir.memory import Realloc
+from pairs.ir.variables import Var
class Arrays:
diff --git a/ir/assign.py b/src/pairs/ir/assign.py
similarity index 83%
rename from ir/assign.py
rename to src/pairs/ir/assign.py
index 4465699..97af6ea 100644
--- a/ir/assign.py
+++ b/src/pairs/ir/assign.py
@@ -1,8 +1,8 @@
-from ir.ast_node import ASTNode
-from ir.data_types import Type_Vector
-from ir.lit import as_lit_ast
-from ir.vector_expr import VectorExpression
from functools import reduce
+from pairs.ir.ast_node import ASTNode
+from pairs.ir.data_types import Type_Vector
+from pairs.ir.lit import as_lit_ast
+from pairs.ir.vector_expr import VectorExpression
class Assign(ASTNode):
diff --git a/ir/ast_node.py b/src/pairs/ir/ast_node.py
similarity index 88%
rename from ir/ast_node.py
rename to src/pairs/ir/ast_node.py
index cbfc0f4..94e75fa 100644
--- a/ir/ast_node.py
+++ b/src/pairs/ir/ast_node.py
@@ -1,4 +1,4 @@
-from ir.data_types import Type_Invalid
+from pairs.ir.data_types import Type_Invalid
class ASTNode:
diff --git a/ir/bin_op.py b/src/pairs/ir/bin_op.py
similarity index 96%
rename from ir/bin_op.py
rename to src/pairs/ir/bin_op.py
index 46c3e4d..95f48dc 100644
--- a/ir/bin_op.py
+++ b/src/pairs/ir/bin_op.py
@@ -1,8 +1,8 @@
-from ir.ast_node import ASTNode
-from ir.assign import Assign
-from ir.data_types import Type_Float, Type_Bool, Type_Vector
-from ir.lit import as_lit_ast
-from ir.vector_expr import VectorExpression
+from pairs.ir.ast_node import ASTNode
+from pairs.ir.assign import Assign
+from pairs.ir.data_types import Type_Float, Type_Bool, Type_Vector
+from pairs.ir.lit import as_lit_ast
+from pairs.ir.vector_expr import VectorExpression
class Decl(ASTNode):
diff --git a/ir/block.py b/src/pairs/ir/block.py
similarity index 97%
rename from ir/block.py
rename to src/pairs/ir/block.py
index b136db8..853de45 100644
--- a/ir/block.py
+++ b/src/pairs/ir/block.py
@@ -1,4 +1,4 @@
-from ir.ast_node import ASTNode
+from pairs.ir.ast_node import ASTNode
class Block(ASTNode):
diff --git a/ir/branches.py b/src/pairs/ir/branches.py
similarity index 92%
rename from ir/branches.py
rename to src/pairs/ir/branches.py
index 224e671..93962ad 100644
--- a/ir/branches.py
+++ b/src/pairs/ir/branches.py
@@ -1,6 +1,6 @@
-from ir.ast_node import ASTNode
-from ir.block import Block
-from ir.lit import as_lit_ast
+from pairs.ir.ast_node import ASTNode
+from pairs.ir.block import Block
+from pairs.ir.lit import as_lit_ast
class Branch(ASTNode):
diff --git a/ir/cast.py b/src/pairs/ir/cast.py
similarity index 86%
rename from ir/cast.py
rename to src/pairs/ir/cast.py
index 7207b10..061eb47 100644
--- a/ir/cast.py
+++ b/src/pairs/ir/cast.py
@@ -1,5 +1,5 @@
-from ir.bin_op import ASTTerm
-from ir.data_types import Type_Int, Type_Float
+from pairs.ir.bin_op import ASTTerm
+from pairs.ir.data_types import Type_Int, Type_Float
class Cast(ASTTerm):
diff --git a/ir/data_types.py b/src/pairs/ir/data_types.py
similarity index 100%
rename from ir/data_types.py
rename to src/pairs/ir/data_types.py
diff --git a/ir/functions.py b/src/pairs/ir/functions.py
similarity index 85%
rename from ir/functions.py
rename to src/pairs/ir/functions.py
index 046cd77..8b01b90 100644
--- a/ir/functions.py
+++ b/src/pairs/ir/functions.py
@@ -1,6 +1,6 @@
-from ir.bin_op import ASTTerm
-from ir.data_types import Type_Int, Type_Invalid
-from ir.lit import as_lit_ast
+from pairs.ir.bin_op import ASTTerm
+from pairs.ir.data_types import Type_Int, Type_Invalid
+from pairs.ir.lit import as_lit_ast
class Call(ASTTerm):
diff --git a/ir/layouts.py b/src/pairs/ir/layouts.py
similarity index 100%
rename from ir/layouts.py
rename to src/pairs/ir/layouts.py
diff --git a/ir/lit.py b/src/pairs/ir/lit.py
similarity index 88%
rename from ir/lit.py
rename to src/pairs/ir/lit.py
index ab62157..ff738b5 100644
--- a/ir/lit.py
+++ b/src/pairs/ir/lit.py
@@ -1,5 +1,5 @@
-from ir.ast_node import ASTNode
-from ir.data_types import Type_Invalid, Type_Int, Type_Float, Type_Bool, Type_String, Type_Vector
+from pairs.ir.ast_node import ASTNode
+from pairs.ir.data_types import Type_Invalid, Type_Int, Type_Float, Type_Bool, Type_String, Type_Vector
def is_literal(a):
diff --git a/ir/loops.py b/src/pairs/ir/loops.py
similarity index 93%
rename from ir/loops.py
rename to src/pairs/ir/loops.py
index 0243dcf..40d73d2 100644
--- a/ir/loops.py
+++ b/src/pairs/ir/loops.py
@@ -1,9 +1,9 @@
-from ir.ast_node import ASTNode
-from ir.bin_op import BinOp, ASTTerm
-from ir.block import Block
-from ir.branches import Filter
-from ir.data_types import Type_Int
-from ir.lit import as_lit_ast
+from pairs.ir.ast_node import ASTNode
+from pairs.ir.bin_op import BinOp, ASTTerm
+from pairs.ir.block import Block
+from pairs.ir.branches import Filter
+from pairs.ir.data_types import Type_Int
+from pairs.ir.lit import as_lit_ast
class Iter(ASTTerm):
diff --git a/ir/math.py b/src/pairs/ir/math.py
similarity index 89%
rename from ir/math.py
rename to src/pairs/ir/math.py
index 93d6269..9ef762f 100644
--- a/ir/math.py
+++ b/src/pairs/ir/math.py
@@ -1,5 +1,5 @@
-from ir.bin_op import ASTTerm
-from ir.data_types import Type_Int, Type_Float
+from pairs.ir.bin_op import ASTTerm
+from pairs.ir.data_types import Type_Int, Type_Float
class Sqrt(ASTTerm):
diff --git a/ir/memory.py b/src/pairs/ir/memory.py
similarity index 88%
rename from ir/memory.py
rename to src/pairs/ir/memory.py
index 21b0ace..72cd1f0 100644
--- a/ir/memory.py
+++ b/src/pairs/ir/memory.py
@@ -1,8 +1,8 @@
-from ir.ast_node import ASTNode
-from ir.bin_op import BinOp
-from ir.sizeof import Sizeof
from functools import reduce
import operator
+from pairs.ir.ast_node import ASTNode
+from pairs.ir.bin_op import BinOp
+from pairs.ir.sizeof import Sizeof
class Malloc(ASTNode):
diff --git a/ir/mutator.py b/src/pairs/ir/mutator.py
similarity index 100%
rename from ir/mutator.py
rename to src/pairs/ir/mutator.py
diff --git a/src/pairs/ir/operators.py b/src/pairs/ir/operators.py
new file mode 100644
index 0000000..e69de29
diff --git a/ir/properties.py b/src/pairs/ir/properties.py
similarity index 94%
rename from ir/properties.py
rename to src/pairs/ir/properties.py
index 2d5be92..c17c78a 100644
--- a/ir/properties.py
+++ b/src/pairs/ir/properties.py
@@ -1,10 +1,10 @@
-from ir.ast_node import ASTNode
-from ir.assign import Assign
-from ir.bin_op import BinOp, Decl, ASTTerm, VectorAccess
-from ir.data_types import Type_Vector
-from ir.layouts import Layout_AoS
-from ir.lit import as_lit_ast
-from ir.vector_expr import VectorExpression
+from pairs.ir.ast_node import ASTNode
+from pairs.ir.assign import Assign
+from pairs.ir.bin_op import BinOp, Decl, ASTTerm, VectorAccess
+from pairs.ir.data_types import Type_Vector
+from pairs.ir.layouts import Layout_AoS
+from pairs.ir.lit import as_lit_ast
+from pairs.ir.vector_expr import VectorExpression
class Properties:
diff --git a/ir/select.py b/src/pairs/ir/select.py
similarity index 77%
rename from ir/select.py
rename to src/pairs/ir/select.py
index 0079d2f..8e5e3ae 100644
--- a/ir/select.py
+++ b/src/pairs/ir/select.py
@@ -1,6 +1,6 @@
-from ir.ast_node import ASTNode
-from ir.bin_op import BinOp
-from ir.lit import as_lit_ast
+from pairs.ir.ast_node import ASTNode
+from pairs.ir.bin_op import BinOp
+from pairs.ir.lit import as_lit_ast
class Select(ASTNode):
diff --git a/ir/sizeof.py b/src/pairs/ir/sizeof.py
similarity index 69%
rename from ir/sizeof.py
rename to src/pairs/ir/sizeof.py
index 9d042bb..4072313 100644
--- a/ir/sizeof.py
+++ b/src/pairs/ir/sizeof.py
@@ -1,5 +1,5 @@
-from ir.bin_op import ASTTerm
-from ir.data_types import Type_Int
+from pairs.ir.bin_op import ASTTerm
+from pairs.ir.data_types import Type_Int
class Sizeof(ASTTerm):
diff --git a/ir/transform.py b/src/pairs/ir/transform.py
similarity index 92%
rename from ir/transform.py
rename to src/pairs/ir/transform.py
index ba738b6..4705552 100644
--- a/ir/transform.py
+++ b/src/pairs/ir/transform.py
@@ -1,10 +1,10 @@
-from ir.arrays import ArrayAccess
-from ir.bin_op import BinOp
-from ir.data_types import Type_Int, Type_Vector
-from ir.layouts import Layout_AoS, Layout_SoA
-from ir.lit import Lit
-from ir.loops import Iter
-from ir.properties import Property
+from pairs.ir.arrays import ArrayAccess
+from pairs.ir.bin_op import BinOp
+from pairs.ir.data_types import Type_Int, Type_Vector
+from pairs.ir.layouts import Layout_AoS, Layout_SoA
+from pairs.ir.lit import Lit
+from pairs.ir.loops import Iter
+from pairs.ir.properties import Property
class Transform:
diff --git a/ir/utils.py b/src/pairs/ir/utils.py
similarity index 82%
rename from ir/utils.py
rename to src/pairs/ir/utils.py
index a4446f1..8151d68 100644
--- a/ir/utils.py
+++ b/src/pairs/ir/utils.py
@@ -1,4 +1,4 @@
-from ir.ast_node import ASTNode
+from pairs.ir.ast_node import ASTNode
class Print(ASTNode):
diff --git a/ir/variables.py b/src/pairs/ir/variables.py
similarity index 93%
rename from ir/variables.py
rename to src/pairs/ir/variables.py
index b4b40da..9f456e8 100644
--- a/ir/variables.py
+++ b/src/pairs/ir/variables.py
@@ -1,6 +1,6 @@
-from ir.ast_node import ASTNode
-from ir.assign import Assign
-from ir.bin_op import ASTTerm
+from pairs.ir.ast_node import ASTNode
+from pairs.ir.assign import Assign
+from pairs.ir.bin_op import ASTTerm
class Variables:
diff --git a/ir/vector_expr.py b/src/pairs/ir/vector_expr.py
similarity index 92%
rename from ir/vector_expr.py
rename to src/pairs/ir/vector_expr.py
index bd3bb0b..706a07d 100644
--- a/ir/vector_expr.py
+++ b/src/pairs/ir/vector_expr.py
@@ -1,6 +1,6 @@
-from ir.ast_node import ASTNode
-from ir.data_types import Type_Vector
-from ir.lit import Lit
+from pairs.ir.ast_node import ASTNode
+from pairs.ir.data_types import Type_Vector
+from pairs.ir.lit import Lit
class VectorExpression(ASTNode):
diff --git a/ir/visitor.py b/src/pairs/ir/visitor.py
similarity index 100%
rename from ir/visitor.py
rename to src/pairs/ir/visitor.py
diff --git a/src/pairs/mapping/.funcs.py.swp b/src/pairs/mapping/.funcs.py.swp
new file mode 100644
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z!}eOF?hy2j)4(Nrww5Iy3QU<zxgwL(9#YDL^xl^cl_93oyd<G}FVnO&rG2GMS60xu
K*PC2ifqejCHIIA%
literal 0
HcmV?d00001
diff --git a/src/pairs/mapping/__init__.py b/src/pairs/mapping/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/new_syntax.py b/src/pairs/mapping/funcs.py
similarity index 75%
rename from new_syntax.py
rename to src/pairs/mapping/funcs.py
index bdbeb0d..7b47ec6 100644
--- a/new_syntax.py
+++ b/src/pairs/mapping/funcs.py
@@ -1,30 +1,7 @@
-import pairs
-from ir.assign import Assign
-from ir.bin_op import BinOp
import ast
import inspect
-
-
-def delta(i, j):
- return position[i] - position[j]
-
-
-def rsq(i, j):
- dp = delta(i, j)
- return dp.x() * dp.x() + dp.y() * dp.y() + dp.z() * dp.z()
-
-
-def lj(i, j):
- sr2 = 1.0 / rsq
- sr6 = sr2 * sr2 * sr2 * sigma6
- #f = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon
- #force[i] += delta * f
- force[i] += delta * 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon
-
-
-def euler(i):
- velocity[i] += dt * force[i] / mass[i]
- position[i] += dt * velocity[i]
+from pairs.ir.assign import Assign
+from pairs.ir.bin_op import BinOp
class UndefinedSymbol():
@@ -142,7 +119,7 @@ class BuildParticleIR(ast.NodeVisitor):
return self.visit(node.value)[self.visit(node.slice)]
-def add_kernel(sim, func, cutoff_radius=None, position=None, symbols={}):
+def compute(sim, func, cutoff_radius=None, position=None, symbols={}):
src = inspect.getsource(func)
tree = ast.parse(src, mode='exec')
#print(ast.dump(ast.parse(src, mode='exec')))
@@ -162,33 +139,9 @@ def add_kernel(sim, func, cutoff_radius=None, position=None, symbols={}):
ir.visit(tree)
elif nparams == 2:
- for i, j, delta, rsq in psim.particle_pairs(cutoff_radius, sim.property(position)):
+ for i, j, delta, rsq in sim.particle_pairs(cutoff_radius, sim.property(position)):
ir.add_symbols({params[0]: i, params[1]: j, 'delta': delta, 'rsq': rsq})
ir.visit(tree)
else:
raise Exception(f"Invalid number of parameters: {nparams}")
-
-
-dt = 0.005
-cutoff_radius = 2.5
-skin = 0.3
-sigma = 1.0
-epsilon = 1.0
-sigma6 = sigma ** 6
-
-psim = pairs.simulation("lj_ns")
-psim.add_real_property('mass', 1.0)
-psim.add_vector_property('position')
-psim.add_vector_property('velocity')
-psim.add_vector_property('force', vol=True)
-psim.from_file("data/minimd_setup_4x4x4.input", ['mass', 'position', 'velocity'])
-psim.create_cell_lists(2.8, 2.8)
-psim.create_neighbor_lists()
-psim.periodic(2.8)
-psim.vtk_output("output/test")
-
-add_kernel(psim, lj, cutoff_radius, 'position', {'sigma6': sigma6, 'epsilon': epsilon})
-add_kernel(psim, euler, symbols={'dt': dt})
-
-psim.generate()
diff --git a/src/pairs/runtime/__init__.py b/src/pairs/runtime/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/runtime/pairs.hpp b/src/pairs/runtime/pairs.hpp
similarity index 100%
rename from runtime/pairs.hpp
rename to src/pairs/runtime/pairs.hpp
diff --git a/runtime/read_from_file.hpp b/src/pairs/runtime/read_from_file.hpp
similarity index 100%
rename from runtime/read_from_file.hpp
rename to src/pairs/runtime/read_from_file.hpp
diff --git a/runtime/vtk.hpp b/src/pairs/runtime/vtk.hpp
similarity index 100%
rename from runtime/vtk.hpp
rename to src/pairs/runtime/vtk.hpp
diff --git a/src/pairs/sim/__init__.py b/src/pairs/sim/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/sim/arrays.py b/src/pairs/sim/arrays.py
similarity index 82%
rename from sim/arrays.py
rename to src/pairs/sim/arrays.py
index 7406019..232964a 100644
--- a/sim/arrays.py
+++ b/src/pairs/sim/arrays.py
@@ -1,5 +1,5 @@
-from ir.memory import Malloc
-from ir.arrays import ArrayDecl
+from pairs.ir.memory import Malloc
+from pairs.ir.arrays import ArrayDecl
class ArraysDecl:
diff --git a/sim/cell_lists.py b/src/pairs/sim/cell_lists.py
similarity index 93%
rename from sim/cell_lists.py
rename to src/pairs/sim/cell_lists.py
index 40ec518..6e94efd 100644
--- a/sim/cell_lists.py
+++ b/src/pairs/sim/cell_lists.py
@@ -1,13 +1,13 @@
-from ir.bin_op import BinOp
-from ir.branches import Branch, Filter
-from ir.cast import Cast
-from ir.data_types import Type_Int
-from ir.math import Ceil
-from ir.loops import For, ParticleFor
-from ir.utils import Print
from functools import reduce
-from sim.resize import Resize
import math
+from pairs.ir.bin_op import BinOp
+from pairs.ir.branches import Branch, Filter
+from pairs.ir.cast import Cast
+from pairs.ir.data_types import Type_Int
+from pairs.ir.math import Ceil
+from pairs.ir.loops import For, ParticleFor
+from pairs.ir.utils import Print
+from pairs.sim.resize import Resize
class CellLists:
diff --git a/sim/grid.py b/src/pairs/sim/grid.py
similarity index 97%
rename from sim/grid.py
rename to src/pairs/sim/grid.py
index 0eea7ed..6d71d2f 100644
--- a/sim/grid.py
+++ b/src/pairs/sim/grid.py
@@ -1,4 +1,4 @@
-from ir.data_types import Type_Float
+from pairs.ir.data_types import Type_Float
class Grid:
diff --git a/sim/kernel_wrapper.py b/src/pairs/sim/kernel_wrapper.py
similarity index 87%
rename from sim/kernel_wrapper.py
rename to src/pairs/sim/kernel_wrapper.py
index 7ac32e3..ccf7f5a 100644
--- a/sim/kernel_wrapper.py
+++ b/src/pairs/sim/kernel_wrapper.py
@@ -1,4 +1,4 @@
-from ir.block import Block
+from pairs.ir.block import Block
class KernelWrapper():
diff --git a/sim/lattice.py b/src/pairs/sim/lattice.py
similarity index 95%
rename from sim/lattice.py
rename to src/pairs/sim/lattice.py
index b9985e6..d2332c7 100644
--- a/sim/lattice.py
+++ b/src/pairs/sim/lattice.py
@@ -1,5 +1,5 @@
-from ir.data_types import Type_Vector
-from ir.loops import For
+from pairs.ir.data_types import Type_Vector
+from pairs.ir.loops import For
class ParticleLattice():
diff --git a/sim/neighbor_lists.py b/src/pairs/sim/neighbor_lists.py
similarity index 89%
rename from sim/neighbor_lists.py
rename to src/pairs/sim/neighbor_lists.py
index f2fa90b..f134c1d 100644
--- a/sim/neighbor_lists.py
+++ b/src/pairs/sim/neighbor_lists.py
@@ -1,8 +1,8 @@
-from ir.branches import Branch, Filter
-from ir.data_types import Type_Int
-from ir.loops import For, ParticleFor, NeighborFor
-from ir.utils import Print
-from sim.resize import Resize
+from pairs.ir.branches import Branch, Filter
+from pairs.ir.data_types import Type_Int
+from pairs.ir.loops import For, ParticleFor, NeighborFor
+from pairs.ir.utils import Print
+from pairs.sim.resize import Resize
class NeighborLists:
diff --git a/sim/particle_simulation.py b/src/pairs/sim/particle_simulation.py
similarity index 82%
rename from sim/particle_simulation.py
rename to src/pairs/sim/particle_simulation.py
index 9bf20a5..2eb5c89 100644
--- a/sim/particle_simulation.py
+++ b/src/pairs/sim/particle_simulation.py
@@ -1,29 +1,30 @@
-from ir.arrays import Arrays
-from ir.block import Block
-from ir.branches import Filter
-from ir.data_types import Type_Int, Type_Float, Type_Vector
-from ir.layouts import Layout_AoS
-from ir.loops import ParticleFor, NeighborFor
-from ir.properties import Properties
-from ir.variables import Variables
-from graph.graphviz import ASTGraph
-from sim.arrays import ArraysDecl
-from sim.cell_lists import CellLists, CellListsBuild, CellListsStencilBuild
-from sim.grid import Grid2D, Grid3D
-from sim.kernel_wrapper import KernelWrapper
-from sim.lattice import ParticleLattice
-from sim.neighbor_lists import NeighborLists, NeighborListsBuild
-from sim.pbc import PBC, UpdatePBC, EnforcePBC, SetupPBC
-from sim.properties import PropertiesAlloc, PropertiesResetVolatile
-from sim.read_from_file import ReadFromFile
-from sim.setup_wrapper import SetupWrapper
-from sim.timestep import Timestep
-from sim.variables import VariablesDecl
-from sim.vtk import VTKWrite
-from transformations.prioritize_scalar_ops import prioritaze_scalar_ops
-from transformations.set_used_bin_ops import set_used_bin_ops
-from transformations.simplify import simplify_expressions
-from transformations.LICM import move_loop_invariant_code
+from pairs.ir.arrays import Arrays
+from pairs.ir.block import Block
+from pairs.ir.branches import Filter
+from pairs.ir.data_types import Type_Int, Type_Float, Type_Vector
+from pairs.ir.layouts import Layout_AoS
+from pairs.ir.loops import ParticleFor, NeighborFor
+from pairs.ir.properties import Properties
+from pairs.ir.variables import Variables
+from pairs.graph.graphviz import ASTGraph
+from pairs.mapping.funcs import compute
+from pairs.sim.arrays import ArraysDecl
+from pairs.sim.cell_lists import CellLists, CellListsBuild, CellListsStencilBuild
+from pairs.sim.grid import Grid2D, Grid3D
+from pairs.sim.kernel_wrapper import KernelWrapper
+from pairs.sim.lattice import ParticleLattice
+from pairs.sim.neighbor_lists import NeighborLists, NeighborListsBuild
+from pairs.sim.pbc import PBC, UpdatePBC, EnforcePBC, SetupPBC
+from pairs.sim.properties import PropertiesAlloc, PropertiesResetVolatile
+from pairs.sim.read_from_file import ReadFromFile
+from pairs.sim.setup_wrapper import SetupWrapper
+from pairs.sim.timestep import Timestep
+from pairs.sim.variables import VariablesDecl
+from pairs.sim.vtk import VTKWrite
+from pairs.transformations.prioritize_scalar_ops import prioritaze_scalar_ops
+from pairs.transformations.set_used_bin_ops import set_used_bin_ops
+from pairs.transformations.simplify import simplify_expressions
+from pairs.transformations.LICM import move_loop_invariant_code
class ParticleSimulation:
@@ -128,6 +129,9 @@ class ParticleSimulation:
self.properties.add_capacity(self.pbc.pbc_capacity)
return self.pbc
+ def compute(self, sim, func, cutoff_radius=None, position=None, symbols={}):
+ return compute(sim, func, cutoff_radius, position, symbols)
+
def particle_pairs(self, cutoff_radius=None, position=None):
self.clear_block()
for i in ParticleFor(self):
diff --git a/sim/pbc.py b/src/pairs/sim/pbc.py
similarity index 94%
rename from sim/pbc.py
rename to src/pairs/sim/pbc.py
index 1f066be..c480c4d 100644
--- a/sim/pbc.py
+++ b/src/pairs/sim/pbc.py
@@ -1,9 +1,9 @@
-from ir.branches import Branch, Filter
-from ir.data_types import Type_Int
-from ir.loops import For, ParticleFor
-from ir.utils import Print
-from ir.select import Select
-from sim.resize import Resize
+from pairs.ir.branches import Branch, Filter
+from pairs.ir.data_types import Type_Int
+from pairs.ir.loops import For, ParticleFor
+from pairs.ir.utils import Print
+from pairs.ir.select import Select
+from pairs.sim.resize import Resize
class PBC:
diff --git a/sim/properties.py b/src/pairs/sim/properties.py
similarity index 84%
rename from sim/properties.py
rename to src/pairs/sim/properties.py
index eca3617..7839eed 100644
--- a/sim/properties.py
+++ b/src/pairs/sim/properties.py
@@ -1,9 +1,9 @@
+from pairs.ir.data_types import Type_Float, Type_Vector
+from pairs.ir.loops import ParticleFor
+from pairs.ir.memory import Malloc, Realloc
+from pairs.ir.properties import RegisterProperty, UpdateProperty
+from pairs.ir.utils import Print
from functools import reduce
-from ir.data_types import Type_Float, Type_Vector
-from ir.loops import ParticleFor
-from ir.memory import Malloc, Realloc
-from ir.properties import RegisterProperty, UpdateProperty
-from ir.utils import Print
import operator
diff --git a/sim/read_from_file.py b/src/pairs/sim/read_from_file.py
similarity index 81%
rename from sim/read_from_file.py
rename to src/pairs/sim/read_from_file.py
index 6a597a2..dc3355b 100644
--- a/sim/read_from_file.py
+++ b/src/pairs/sim/read_from_file.py
@@ -1,7 +1,7 @@
-from ir.data_types import Type_Float
-from ir.functions import Call_Int
-from ir.properties import PropertyList
-from sim.grid import MutableGrid
+from pairs.ir.data_types import Type_Float
+from pairs.ir.functions import Call_Int
+from pairs.ir.properties import PropertyList
+from pairs.sim.grid import MutableGrid
class ReadFromFile():
diff --git a/sim/resize.py b/src/pairs/sim/resize.py
similarity index 84%
rename from sim/resize.py
rename to src/pairs/sim/resize.py
index f862578..308ceaa 100644
--- a/sim/resize.py
+++ b/src/pairs/sim/resize.py
@@ -1,10 +1,10 @@
+from pairs.ir.branches import Filter
+from pairs.ir.data_types import Type_Int, Type_Float, Type_Vector
+from pairs.ir.loops import While
+from pairs.ir.memory import Realloc
+from pairs.ir.properties import UpdateProperty
+from pairs.ir.utils import Print
from functools import reduce
-from ir.branches import Filter
-from ir.data_types import Type_Int, Type_Float, Type_Vector
-from ir.loops import While
-from ir.memory import Realloc
-from ir.properties import UpdateProperty
-from ir.utils import Print
import operator
diff --git a/sim/setup_wrapper.py b/src/pairs/sim/setup_wrapper.py
similarity index 87%
rename from sim/setup_wrapper.py
rename to src/pairs/sim/setup_wrapper.py
index bc0d535..6297667 100644
--- a/sim/setup_wrapper.py
+++ b/src/pairs/sim/setup_wrapper.py
@@ -1,4 +1,4 @@
-from ir.block import Block
+from pairs.ir.block import Block
class SetupWrapper():
diff --git a/sim/timestep.py b/src/pairs/sim/timestep.py
similarity index 91%
rename from sim/timestep.py
rename to src/pairs/sim/timestep.py
index f15ee7c..3e312f2 100644
--- a/sim/timestep.py
+++ b/src/pairs/sim/timestep.py
@@ -1,7 +1,7 @@
-from ir.bin_op import BinOp
-from ir.block import Block
-from ir.branches import Branch
-from ir.loops import For
+from pairs.ir.bin_op import BinOp
+from pairs.ir.block import Block
+from pairs.ir.branches import Branch
+from pairs.ir.loops import For
class Timestep:
diff --git a/sim/variables.py b/src/pairs/sim/variables.py
similarity index 85%
rename from sim/variables.py
rename to src/pairs/sim/variables.py
index 4d37e32..6869ed1 100644
--- a/sim/variables.py
+++ b/src/pairs/sim/variables.py
@@ -1,4 +1,4 @@
-from ir.variables import VarDecl
+from pairs.ir.variables import VarDecl
class VariablesDecl:
diff --git a/sim/vtk.py b/src/pairs/sim/vtk.py
similarity index 84%
rename from sim/vtk.py
rename to src/pairs/sim/vtk.py
index c499726..86de551 100644
--- a/sim/vtk.py
+++ b/src/pairs/sim/vtk.py
@@ -1,6 +1,6 @@
-from ir.ast_node import ASTNode
-from ir.functions import Call_Void
-from ir.lit import as_lit_ast
+from pairs.ir.ast_node import ASTNode
+from pairs.ir.functions import Call_Void
+from pairs.ir.lit import as_lit_ast
class VTKWrite(ASTNode):
diff --git a/transformations/LICM.py b/src/pairs/transformations/LICM.py
similarity index 97%
rename from transformations/LICM.py
rename to src/pairs/transformations/LICM.py
index 0ac4d37..264aa37 100644
--- a/transformations/LICM.py
+++ b/src/pairs/transformations/LICM.py
@@ -1,8 +1,8 @@
-from ir.bin_op import BinOp
-from ir.loops import For, While
-from ir.mutator import Mutator
-from ir.properties import PropertyAccess
-from ir.visitor import Visitor
+from pairs.ir.bin_op import BinOp
+from pairs.ir.loops import For, While
+from pairs.ir.mutator import Mutator
+from pairs.ir.properties import PropertyAccess
+from pairs.ir.visitor import Visitor
class SetBlockVariants(Mutator):
diff --git a/src/pairs/transformations/__init__.py b/src/pairs/transformations/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/transformations/prioritize_scalar_ops.py b/src/pairs/transformations/prioritize_scalar_ops.py
similarity index 93%
rename from transformations/prioritize_scalar_ops.py
rename to src/pairs/transformations/prioritize_scalar_ops.py
index cf099a8..47957f6 100644
--- a/transformations/prioritize_scalar_ops.py
+++ b/src/pairs/transformations/prioritize_scalar_ops.py
@@ -1,6 +1,6 @@
-from ir.bin_op import BinOp
-from ir.data_types import Type_Float, Type_Vector
-from ir.mutator import Mutator
+from pairs.ir.bin_op import BinOp
+from pairs.ir.data_types import Type_Float, Type_Vector
+from pairs.ir.mutator import Mutator
class PrioritazeScalarOps(Mutator):
diff --git a/transformations/set_used_bin_ops.py b/src/pairs/transformations/set_used_bin_ops.py
similarity index 93%
rename from transformations/set_used_bin_ops.py
rename to src/pairs/transformations/set_used_bin_ops.py
index 404cb65..ac26bf1 100644
--- a/transformations/set_used_bin_ops.py
+++ b/src/pairs/transformations/set_used_bin_ops.py
@@ -1,4 +1,4 @@
-from ir.visitor import Visitor
+from pairs.ir.visitor import Visitor
class SetUsedBinOps(Visitor):
diff --git a/transformations/simplify.py b/src/pairs/transformations/simplify.py
similarity index 90%
rename from transformations/simplify.py
rename to src/pairs/transformations/simplify.py
index 69803d8..ecba0d6 100644
--- a/transformations/simplify.py
+++ b/src/pairs/transformations/simplify.py
@@ -1,6 +1,6 @@
-from ir.data_types import Type_Int
-from ir.lit import Lit
-from ir.mutator import Mutator
+from pairs.ir.data_types import Type_Int
+from pairs.ir.lit import Lit
+from pairs.ir.mutator import Mutator
class SimplifyExpressions(Mutator):
--
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