Added continuation for stopped simulation

scripts/check_width_exists.py

@@ -1,23 +0,0 @@
-from pathlib import Path
-import numpy as np, pickle, sys
-
-from squish import Simulation
-
-def main():
-	n = int(sys.argv[1])
-	all_widths = set(np.round(np.arange(3, 10.05, 0.05), 2))
-	for file in Path(f"squish_output/Radial[T]Search - N{n} - 500").iterdir():
-		sim, frames = Simulation.load(file / 'data.squish')
-
-		if sim.domain.n == n:
-			try:
-				all_widths.remove(next(frames)["domain"][1])
-			except StopIteration:
-				pass
-
-	remain_widths = sorted(list(all_widths))[::-1]
-	print("Remaining:", remain_widths)
-
-
-if __name__ == "__main__":
-	main()

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = squish
-version = 0.1.3
+version = 0.1.4
 author = Kenneth Jao
 author_email = ksjdragon@gmail.com
 description = squish is Python program which perform simulations for the flow of 'soft' or 'compressible' objects under some energy in a periodic domain.

squish/common.py

@@ -6,7 +6,6 @@ from pathlib import Path
 from ._squish import VoronoiContainer, AreaEnergy, RadialALEnergy, RadialTEnergy
 
 OUTPUT_DIR = Path("squish_output")
-OUTPUT_DIR.mkdir(exist_ok=True)
 
 STR_TO_ENERGY = {
 	"area": AreaEnergy,
@@ -17,7 +16,7 @@ STR_TO_ENERGY = {
 
 def generate_filepath(sim: SimulationMode, fol: Union[str, Path], prec: int = 2) -> Path:
 	energy = sim.energy.title_str
-	width, height = round(sim.domain.w, 2), round(sim.domain.h, 2)
+	width, height = round(sim.domain.w, prec), round(sim.domain.h, prec)
 
 	base_path = f"{fol}/{energy}{sim.title_str} - " + \
 					f"N{sim.domain.n} - {width:.{prec}f}x{height:.{prec}f}"

squish/diagram.py

@@ -6,7 +6,7 @@ from matplotlib.ticker import MaxNLocator, FormatStrFormatter
 from scipy.spatial import Voronoi, voronoi_plot_2d
 from multiprocessing import Pool, cpu_count
 
-from .common import DomainParams
+from .common import DomainParams, OUTPUT_DIR
 
 SYMM = np.array([[0,0], [1,0], [1,1], [0,1], [-1,1], [-1,0], [-1,-1], [0,-1], [1,-1]])
 
@@ -302,6 +302,8 @@ class Diagram:
 
 
 	def render_frames(self, frames: List[int], fol: str = 'frames') -> None:
+		OUTPUT_DIR.mkdir(exist_ok=True)
+		self.sim.path.mkdir(exist_ok=True)
 		(self.sim.path / fol).mkdir(exist_ok=True)
 		combo_list = []
 		for i in range(cpu_count()):

squish/simulation.py

@@ -5,6 +5,7 @@ import pickle, numpy as np
 from math import log10
 from scipy.linalg import null_space
 from timeit import default_timer as timer
+from pathlib import Path
 
 from .common import DomainParams, Energy, generate_filepath, OUTPUT_DIR
 
@@ -46,7 +47,7 @@ class Simulation:
 		return len(self.frames)
 
 
-	def add_frame(self, points: Optional[numpy.ndarray]) -> None:
+	def add_frame(self, points: Optional[numpy.ndarray] = None) -> None:
 		if points is None:
 			points = np.random.random_sample((self.domain.n, 2)) * self.domain.dim
 		else:
@@ -91,6 +92,7 @@ class Simulation:
 
 
 	def save(self, info: Dict, overwrite: bool = False) -> None:
+		OUTPUT_DIR.mkdir(exist_ok=True)
 		self.path.mkdir(exist_ok=True)
 		path = self.path / 'data.squish'
 
@@ -117,8 +119,9 @@ class Simulation:
 
 	@staticmethod
 	def load(path: str) -> Tuple[Simulation, Generator]:
+		path = Path(path)
 		def frames() -> Dict:
-			with open(path, 'rb') as infile:
+			with open(path / 'data.squish', 'rb') as infile:
 				first = True
 				while True:
 					try:
@@ -130,16 +133,26 @@ class Simulation:
 					except EOFError:
 						break
 
-		with open(path, 'rb') as infile:
+		with open(path / 'data.squish', 'rb') as infile:
 			sim_info = pickle.load(infile)
 
 			domain = DomainParams(*sim_info["domain"])
 			energy = Energy(sim_info["energy"])
 			sim = STR_TO_SIM[sim_info["mode"]](domain, energy, *list(sim_info.values())[3:])
+			sim.path = path
 
 			return sim, frames()
 
 
+	@staticmethod
+	def from_file(path: str) -> Simulation:
+		sim, frames = Simulation.load(path)
+		for frame in frames:
+			sim.frames.append(sim.energy.mode(*frame["domain"], frame["arr"]))
+
+		return sim
+
+
 class Flow(Simulation):
 	"""Finds an equilibrium from initial sites.
 
@@ -177,12 +190,13 @@ class Flow(Simulation):
 		return info
 
 
-	def run(self, save: bool, log: bool, log_steps: int) -> None:
+	def run(self, save: bool, log: bool, log_steps: int,
+			new_sites: Optional[numpy.ndarray] = None) -> None:
 		if log: print(f"Find - {self.domain}", flush=True)
-		if save: self.save(self.initial_data, True)
+		if save and len(self) == 0: self.save(self.initial_data, True)
-		if len(self) == 0: self.add_frame()
+		if len(self) == 0: self.add_frame(new_sites)
 
-		i, stop = 0, False
+		i, stop = len(self)-1, False
 
 		while not stop:	# Get to threshold.
 			if save:
@@ -262,17 +276,12 @@ class Search(Simulation):
 		return info
 
 
-	def run(self, save: bool, log: bool, log_steps: int) -> None:
+	def run(self, save: bool, log: bool, log_steps: int,
+			new_sites: Optional[numpy.ndarray] = None) -> None:
 		if log: print(f'Travel - {self.domain}', flush=True)
-		if save: self.save(self.initial_data, True)
+		if save and len(self) == 0: self.save(self.initial_data, True)
 
-		if len(self) != 0:
+		for i in range(len(self), self.count):
-			new_sites = self[0].site_arr
-			self.frames = []
-		else:
-			new_sites = None
-
-		for i in range(self.count):
 			# Get to equilibrium.
 			sim = Flow(self.domain, self.energy, self.step_size, self.thres, self.adaptive)
 			sim.add_frame(new_sites)
@@ -298,7 +307,6 @@ class Search(Simulation):
 				new_sites = self.frames[i].add_sites(self.kernel_step*vec)
 
 
-
 class Shrink(Simulation):
 	"""Shrinks width and finds nearest equilibrium.
 
@@ -343,17 +351,12 @@ class Shrink(Simulation):
 		return info
 
 
-	def run(self, save: bool, log: bool, log_steps: int) -> None:
+	def run(self, save: bool, log: bool, log_steps: int,
+			new_sites: Optional[numpy.ndarray] = None) -> None:
 		if log: print(f'Shrink - {self.domain}', flush=True)
-		if save: self.save(self.initial_data, True)
+		if save and len(self) == 0: self.save(self.initial_data, True)
 
-		if len(self) != 0:
+		width = self.domain.w if len(self.frames) == 0 else self.frames[-1].w
-			new_sites = self[0].site_arr
-			self.frames = []
-		else:
-			new_sites = None
-
-		width = self.domain.w
 		i = 0
 		while width >= self.stop_width:
 			# Get to equilibrium.
@@ -371,6 +374,7 @@ class Shrink(Simulation):
 			width -= self.delta
 			i += 1
 
+
 STR_TO_SIM = {
 	"flow": Flow,
 	"search": Search,

squish/squish.py

@@ -5,7 +5,7 @@ from shutil import which
 from pathlib import Path
 
 from .common import DomainParams, Energy
-from .simulation import Flow, Search, Shrink
+from .simulation import Simulation, Flow, Search, Shrink
 from .diagram import Diagram
 
 dia_presets = {
@@ -45,13 +45,15 @@ def check_params(container: Dict, needed: List[str], valid: Dict) -> None:
 
 def main():
 	# Loading configuration and settings.
-	parser = argparse.ArgumentParser("PackSim")
+	parser = argparse.ArgumentParser("Squish")
 	parser.add_argument('sim_conf', metavar='/path/to/config.json',
 						help="configuration file for a simulation")
 	parser.add_argument('-q', '--quiet', dest='quiet', action='store_true', default=False,
 						help="suppress all normal output")
 	parser.add_argument('-l', '--log', dest='log_steps', default=50, type=int,
 						help="number of iterations before logging")
+	parser.add_argument('-i', dest='input_file', metavar='/path/to/sim',
+						help="folder that contains outputted simulation files.", default=None)
 
 	parser.add_argument('--n_objects', dest='n', type=int, help="objects in domain")
 	parser.add_argument('--width', dest='w', type=float, help="width of domain")
@@ -60,17 +62,14 @@ def main():
 	parser.add_argument('--energy', dest='energy', help="energy type of system")
 
 	args = parser.parse_args()
-	config_sim(args)
+	do_sim(args, args.input_file)
-	# if args.input_file is None:
-	# 	config_sim(args)
-	# else:
-	# 	loaded_sim(args)
 
 
-def config_sim(args):
+def do_sim(args, file):
 	with open(args.sim_conf) as f:
 		params = json.load(f)
 
+
 	check_params(params, ["domain", "simulation"], {})
 	dmn_params, sim_params = params["domain"], params["simulation"]
 
@@ -105,20 +104,23 @@ def config_sim(args):
 
 	name = sim_params.get("name")
 
-	if mode == "flow":
+	if file is None:
-		sim = Flow(domain, energy, step, thres, adaptive, name=name)
+		if mode == "flow":
-	elif mode == "search":
+			sim = Flow(domain, energy, step, thres, adaptive, name=name)
-		check_params(sim_params, ["manifold_step_size", "eq_stop_count"], {
+		elif mode == "search":
-			"manifold_step_size": "positive", "eq_stop_count": "positive"
+			check_params(sim_params, ["manifold_step_size", "eq_stop_count"], {
-		})
+				"manifold_step_size": "positive", "eq_stop_count": "positive"
-		sim = Search(domain, energy, step, thres, adaptive, sim_params["manifold_step_size"],
+			})
-						sim_params["eq_stop_count"], name=name)
+			sim = Search(domain, energy, step, thres, adaptive, sim_params["manifold_step_size"],
-	elif mode == "shrink":
+							sim_params["eq_stop_count"], name=name)
-		check_params(sim_params, ["width_change", "width_stop"], {
+		elif mode == "shrink":
-			"width_change": "positive", "width_stop": "positive"
+			check_params(sim_params, ["width_change", "width_stop"], {
-		})
+				"width_change": "positive", "width_stop": "positive"
-		sim = Shrink(domain, energy, step, thres, adaptive, sim_params["width_change"],
+			})
-						sim_params["width_stop"], name=name)
+			sim = Shrink(domain, energy, step, thres, adaptive, sim_params["width_change"],
+							sim_params["width_stop"], name=name)
+	else:
+		sim = Simulation.from_file(file)
 
 	save_diagram = False
 	if "diagram" in params:
@@ -139,8 +141,7 @@ def config_sim(args):
 		if "time" not in dia_params:
 			dia_params["time"] = 30
 
-	sim.add_frame(points)
+	sim.run(save_sim, not args.quiet, args.log_steps, points)
-	sim.run(save_sim, not args.quiet, args.log_steps)
 
 	if save_diagram:
 		diagram = Diagram(sim, dia_params["figures"])
@@ -153,9 +154,6 @@ def config_sim(args):
 				diagram.render_video(dia_params["time"], "use_all")
 
 
-def loaded_sim(args):
-	pass
-
 def pre():
 	os.environ["QT_LOGGING_RULES"] = "*=false"
 	try: