diff --git a/ast/arrays.py b/ast/arrays.py
index 93b718bf6bb88eb6a4cbb8ff0fe8b706842615ea..6908bbe8b0e340bc4d019e00dc755bd3dca77476 100644
--- a/ast/arrays.py
+++ b/ast/arrays.py
@@ -126,6 +126,7 @@ class ArrayAccess:
self.array = array
self.indexes = [as_lit_ast(sim, index)]
self.index = None
+ self.mutable = True
self.generated = False
self.check_and_set_index()
@@ -177,6 +178,9 @@ class ArrayAccess:
return self.array.type()
# return self.array.type() if self.index is None else Type_Array
+ def is_mutable(self):
+ return self.mutable
+
def scope(self):
if self.index is None:
scope = None
diff --git a/ast/block.py b/ast/block.py
index f68f9811b0375698e42148f58c78862e2367c68b..de9e32bd9967ce26244aa4f3dc2f448ad5a85726 100644
--- a/ast/block.py
+++ b/ast/block.py
@@ -68,10 +68,8 @@ class Block:
return fn(self)
def merge_blocks(block1, block2):
- assert isinstance(block1, Block), \
- "First block type is not Block!"
- assert isinstance(block2, Block), \
- "Second block type is not Block!"
+ assert isinstance(block1, Block), "First block type is not Block!"
+ assert isinstance(block2, Block), "Second block type is not Block!"
return Block(block1.sim, block1.statements() + block2.statements())
def from_list(sim, block_list):
@@ -79,8 +77,7 @@ class Block:
result_block = Block(sim, [])
for block in block_list:
- assert isinstance(block, Block), \
- "Element in list is not Block!"
+ assert isinstance(block, Block), "Element in list is not Block!"
result_block = Block.merge_blocks(result_block, block)
return result_block
diff --git a/ast/cast.py b/ast/cast.py
index 970109e06a25556468d34530f076d30961a0cc3f..d219d961b21908f1350beeeaf8609276bf95659f 100644
--- a/ast/cast.py
+++ b/ast/cast.py
@@ -19,6 +19,9 @@ class Cast:
def type(self):
return self.cast_type
+ def is_mutable(self):
+ return self.expr.is_mutable()
+
def scope(self):
return self.expr.scope()
diff --git a/ast/expr.py b/ast/expr.py
index ac889de3b5c27616b250834f34a3b8557495f326..c7ec9f4ba3a429387d9a2624c0fd1053aaa978d0 100644
--- a/ast/expr.py
+++ b/ast/expr.py
@@ -21,6 +21,7 @@ class Expr:
self.expr_type = Expr.infer_type(self.lhs, self.rhs, self.op)
self.expr_scope = None
self.vec_generated = []
+ self.mutable = self.lhs.is_mutable() or self.rhs.is_mutable() # Value can change accross references
self.generated = False
def __str__(self):
@@ -131,6 +132,9 @@ class Expr:
def type(self):
return self.expr_type
+ def is_mutable(self):
+ return self.mutable
+
def scope(self):
if self.expr_scope is None:
lhs_scp = self.lhs.scope()
@@ -186,6 +190,7 @@ class ExprVec():
self.expr = expr
self.index = index
self.expr_scope = None
+ self.mutable = self.expr.is_mutable() or self.index.is_mutable()
self.lhs = (expr.lhs if not isinstance(expr.lhs, Expr)
else ExprVec(sim, expr.lhs, index))
self.rhs = (expr.rhs if not isinstance(expr.rhs, Expr)
@@ -231,6 +236,9 @@ class ExprVec():
def type(self):
return Type_Float
+ def is_mutable(self):
+ return self.mutable
+
def scope(self):
if self.expr_scope is None:
expr_scp = self.expr.scope()
diff --git a/ast/lit.py b/ast/lit.py
index 693c32d463970ddfa248a03019212b4ecb09ac2c..ff09f2397178eeceb8a0dbc8cf9ef96f2c6d5f38 100644
--- a/ast/lit.py
+++ b/ast/lit.py
@@ -48,6 +48,9 @@ class Lit:
def type(self):
return self.lit_type
+ def is_mutable(self):
+ return False
+
def scope(self):
return self.sim.global_scope
diff --git a/ast/loops.py b/ast/loops.py
index acf12d5fde7dee0678018d832f570e17ffc07392..817b6215f08671ed6ab58be5a74ed50b1a885605 100644
--- a/ast/loops.py
+++ b/ast/loops.py
@@ -20,6 +20,9 @@ class Iter():
def type(self):
return Type_Int
+ def is_mutable(self):
+ return False
+
def scope(self):
return self.loop.block
diff --git a/ast/math.py b/ast/math.py
index e234ff2b6d2bce07c9f9d680d1f8ec6462a9393c..bee39951a0894197903867afb999b4b86af66c32 100644
--- a/ast/math.py
+++ b/ast/math.py
@@ -12,6 +12,9 @@ class Sqrt:
def type(self):
return self.expr.type()
+ def is_mutable(self):
+ return self.expr.is_mutable()
+
def scope(self):
return self.expr.scope()
diff --git a/ast/properties.py b/ast/properties.py
index 64c042bedefa68431a3295aaa25edf60376b1064..3e261beb111a66f93cc82226472953e69fb01137 100644
--- a/ast/properties.py
+++ b/ast/properties.py
@@ -46,6 +46,7 @@ class Property:
self.prop_layout = layout
self.default_value = default
self.volatile = volatile
+ self.mutable = True
self.flattened = False
def __str__(self):
@@ -63,6 +64,9 @@ class Property:
def default(self):
return self.default_value
+ def is_mutable(self):
+ return self.mutable
+
def scope(self):
return self.sim.global_scope
diff --git a/ast/sizeof.py b/ast/sizeof.py
index 917328a1b3863e6270ef8f3f480185fc724666b4..df171a81a50fb615f02d74ee4da6314b8eb670da 100644
--- a/ast/sizeof.py
+++ b/ast/sizeof.py
@@ -13,6 +13,9 @@ class Sizeof:
def type(self):
return Type_Int
+ def is_mutable(self):
+ return False
+
def scope(self):
return self.sim.global_scope
diff --git a/ast/transform.py b/ast/transform.py
index bdbb99756e334dc646b410484de7fbeb7a57e636..1dad678fe46eee9210f9c9ac3c508814aadbfd50 100644
--- a/ast/transform.py
+++ b/ast/transform.py
@@ -22,7 +22,8 @@ class Transform:
item = [f for f in Transform.flattened_list if
f[0] == ast.expr.lhs and
f[1] == ast.index and
- f[2] == ast.expr.rhs]
+ f[2] == ast.expr.rhs and
+ not ast.expr.rhs.is_mutable()]
if item:
return item[0][3]
diff --git a/ast/variables.py b/ast/variables.py
index 501f1c92f31922e9c6c976650fcbb4c41bf31cef..9a075eba90d8eda9ce78be3ec3a422a2b28a902a 100644
--- a/ast/variables.py
+++ b/ast/variables.py
@@ -29,6 +29,7 @@ class Var:
self.var_name = var_name
self.var_type = var_type
self.var_init_value = init_value
+ self.mutable = True
self.var_bonded_arrays = []
def __str__(self):
@@ -94,6 +95,9 @@ class Var:
def bonded_arrays(self):
return self.var_bonded_arrays
+ def is_mutable(self):
+ return self.mutable
+
def scope(self):
return self.sim.global_scope
diff --git a/data/minimd_setup_4x4x4.input b/data/minimd_setup_4x4x4.input
new file mode 100644
index 0000000000000000000000000000000000000000..a31ad8693606608786a77d7678f2ef286705d13f
--- /dev/null
+++ b/data/minimd_setup_4x4x4.input
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diff --git a/output/.gitignore b/output/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..5e7d2734cfc60289debf74293817c0a8f572ff32
--- /dev/null
+++ b/output/.gitignore
@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore
diff --git a/particle.py b/particle.py
index 7a4377eb39cf9933a8c41cb3f8816a5885059878..d9b95bf4a97ba01b139f976444d85b500c859864 100644
--- a/particle.py
+++ b/particle.py
@@ -14,9 +14,10 @@ position = psim.add_vector_property('position')
velocity = psim.add_vector_property('velocity')
force = psim.add_vector_property('force', vol=True)
-grid = psim.grid_3d(0.0, 16.0, 0.0, 16.0, 0.0, 16.0)
-psim.create_particle_lattice(grid, spacing=[1.2, 1.2, 1.2])
-psim.create_cell_lists(grid, 2.8, 2.8)
+#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.periodic(2.8)
psim.vtk_output("output/test")
diff --git a/sim/particle_simulation.py b/sim/particle_simulation.py
index 3f3c485d5fa405b7f626bf558c074976f2d1aec5..ce0ba31f55cf86cd666f7413ae7b16bf054ed3f6 100644
--- a/sim/particle_simulation.py
+++ b/sim/particle_simulation.py
@@ -14,6 +14,7 @@ from sim.kernel_wrapper import KernelWrapper
from sim.lattice import ParticleLattice
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
@@ -103,8 +104,14 @@ class ParticleSimulation:
lattice = ParticleLattice(self, grid, spacing, props, positions)
self.setups.add_setup_block(lattice.lower())
- def create_cell_lists(self, grid, spacing, cutoff_radius):
- self.cell_lists = CellLists(self, grid, spacing, cutoff_radius)
+ def from_file(self, filename, prop_names):
+ props = [self.property(prop_name) for prop_name in prop_names]
+ read_object = ReadFromFile(self, filename, props)
+ self.setups.add_setup_block(read_object.lower())
+ self.grid = read_object.grid
+
+ def create_cell_lists(self, spacing, cutoff_radius):
+ self.cell_lists = CellLists(self, self.grid, spacing, cutoff_radius)
return self.cell_lists
def periodic(self, cutneigh, flags=[1, 1, 1]):
@@ -168,8 +175,8 @@ class ParticleSimulation:
def generate(self):
timestep = Timestep(self, self.ntimesteps, [
(EnforcePBC(self.pbc).lower(), 20),
- (SetupPBC(self.pbc).lower(), 20),
- UpdatePBC(self.pbc).lower(),
+ #(SetupPBC(self.pbc).lower(), 20),
+ #UpdatePBC(self.pbc).lower(),
(CellListsBuild(self.cell_lists).lower(), 20),
PropertiesResetVolatile(self).lower(),
self.kernels.lower()
@@ -180,6 +187,10 @@ class ParticleSimulation:
body = Block.from_list(self, [
CellListsStencilBuild(self.cell_lists).lower(),
self.setups.lower(),
+ EnforcePBC(self.pbc).lower(),
+ #SetupPBC(self.pbc).lower(),
+ #UpdatePBC(self.pbc).lower(),
+ CellListsBuild(self.cell_lists).lower(),
Block(self, VTKWrite(self, self.vtk_file, 0)),
timestep.as_block()
])
diff --git a/sim/read_from_file.py b/sim/read_from_file.py
new file mode 100644
index 0000000000000000000000000000000000000000..42608a1161e3e4baa3011939ca3d3527e3875036
--- /dev/null
+++ b/sim/read_from_file.py
@@ -0,0 +1,49 @@
+from ast.data_types import Type_Int, Type_Float, Type_Vector
+from ast.loops import For
+from sim.grid import Grid
+
+class ReadFromFile():
+ def __init__(self, sim, filename, props):
+ self.sim = sim
+ self.filename = filename
+ self.props = props
+ self.grid = None
+
+ def lower(self):
+ ndims = None
+ nlocal = self.sim.nlocal
+ line_number = 0
+
+ self.sim.clear_block()
+ with open(self.filename, "r") as fp:
+ for line in fp:
+ current_data = line.split(',')
+ if line_number == 0:
+ assert len(current_data) % 2 == 0, "Number of dimensions in header must be even!"
+ ndims = int(len(current_data) / 2)
+ config = [[float(current_data[d * 2]), float(current_data[d * 2 + 1])] for d in range(0, ndims)]
+ self.grid = Grid(self.sim, config)
+ else:
+ i = 0
+ for p in self.props:
+ if p.type() == Type_Vector:
+ for d in range(0, ndims):
+ p[nlocal][d].set(float(current_data[i + d]))
+
+ i += ndims
+
+ else:
+ if p.type() == Type_Int:
+ p[nlocal].set(int(current_data[i]))
+ elif p.type() == Type_Float:
+ p[nlocal].set(float(current_data[i]))
+ else:
+ raise Exception(f"Invalid property type at line {line_number}!")
+
+ i += 1
+
+ nlocal.set(nlocal + 1)
+
+ line_number += 1
+
+ return self.sim.block
diff --git a/sim/timestep.py b/sim/timestep.py
index 222fda1cb66ee6d11218e319e7fa1ddd403efe22..3599933bbd2f34a2217418f0f05ebc56dd31b00a 100644
--- a/sim/timestep.py
+++ b/sim/timestep.py
@@ -8,7 +8,7 @@ class Timestep:
def __init__(self, sim, nsteps, item_list=None):
self.sim = sim
self.block = Block(sim, [])
- self.timestep_loop = For(sim, 0, nsteps, self.block)
+ self.timestep_loop = For(sim, 1, nsteps + 1, self.block)
if item_list is not None:
for item in item_list:
@@ -24,9 +24,7 @@ class Timestep:
assert exec_every >= 0, \
"exec_every parameter must be higher or equal than zero!"
- stmts = (item if not isinstance(item, Block)
- else item.statements())
-
+ stmts = item if not isinstance(item, Block) else item.statements()
ts = self.timestep_loop.iter()
if exec_every > 0:
self.block.add_statement(