From 9965a3d5bae73ab0092f1cb442ed4adccd5e87b8 Mon Sep 17 00:00:00 2001 From: Michele Ceriotti Date: Sat, 20 Apr 2024 17:48:59 +0200 Subject: [PATCH] Lint --- ipi/engine/forcefields.py | 25 +++++++++++++------------ ipi/engine/forces.py | 2 +- ipi/inputs/forcefields.py | 9 ++++++--- 3 files changed, 20 insertions(+), 16 deletions(-) diff --git a/ipi/engine/forcefields.py b/ipi/engine/forcefields.py index 502be3fa3..050829176 100644 --- a/ipi/engine/forcefields.py +++ b/ipi/engine/forcefields.py @@ -644,6 +644,7 @@ def evaluate(self, r): r["status"] = "Done" r["t_finished"] = time.time() + class FFPlumed(FFEval): """Direct PLUMED interface @@ -719,21 +720,21 @@ def __init__( self.plumedrestart = True self.plumed.cmd("setRestart", 1) self.plumed.cmd("init") - - ipi_name = lambda name : "ipi_"+name.replace(".","_") + + ipi_name = lambda name: "ipi_" + name.replace(".", "_") self.plumed_data = {} for x in plumedextras: - rank = np.zeros( 1, dtype=np.int_ ) - self.plumed.cmd(f"getDataRank {x}", rank ) - if rank[0]>1: + rank = np.zeros(1, dtype=np.int_) + self.plumed.cmd(f"getDataRank {x}", rank) + if rank[0] > 1: raise ValueError("Cannot retrieve varibles with rank > 1") - shape = np.zeros( rank[0], dtype=np.int_ ) - if shape[0]>1: - raise ValueError("Cannot retrieve varibles with size > 1") - self.plumed.cmd(f"getDataShape {x}", shape ) + shape = np.zeros(rank[0], dtype=np.int_) + if shape[0] > 1: + raise ValueError("Cannot retrieve varibles with size > 1") + self.plumed.cmd(f"getDataShape {x}", shape) self.plumed_data[x] = np.zeros(shape, dtype=np.double) - self.plumed.cmd(f"setMemoryForData {x}", self.plumed_data[x] ) - + self.plumed.cmd(f"setMemoryForData {x}", self.plumed_data[x]) + self.charges = dstrip(myatoms.q) * 0.0 self.masses = dstrip(myatoms.m) self.lastq = np.zeros(3 * self.natoms) @@ -775,7 +776,7 @@ def evaluate(self, r): self.plumed.cmd("setVirial", vir) self.plumed.cmd("prepareCalc") self.plumed.cmd("performCalcNoUpdate") - + bias = np.zeros(1, float) self.plumed.cmd("getBias", bias) v = bias[0] diff --git a/ipi/engine/forces.py b/ipi/engine/forces.py index 5e48a4ad5..199d2af40 100644 --- a/ipi/engine/forces.py +++ b/ipi/engine/forces.py @@ -1448,7 +1448,7 @@ def extra_combine(self): re = {} for k in range(self.nforces): - # combines the extras from the different force components + # combines the extras from the different force components for e, v in self.mforces[k].extras.items(): if e in self.mforces[k].force_extras: # extras that are tagged as force_extras are treated exactly as if they were an energy/force/stress diff --git a/ipi/inputs/forcefields.py b/ipi/inputs/forcefields.py index bb919527b..d11d46b97 100644 --- a/ipi/inputs/forcefields.py +++ b/ipi/inputs/forcefields.py @@ -523,8 +523,11 @@ class InputFFPlumed(InputForceField): ), "plumedextras": ( InputArray, - {"dtype": str, "default": input_default(factory=np.zeros, args=(0, str)), - "help": "List of variables defined in the PLUMED input, that should be transferred to i-PI as `extras` fields." }, + { + "dtype": str, + "default": input_default(factory=np.zeros, args=(0, str)), + "help": "List of variables defined in the PLUMED input, that should be transferred to i-PI as `extras` fields.", + }, ), } @@ -563,7 +566,7 @@ def fetch(self): plumeddat=self.plumeddat.fetch(), plumedstep=self.plumedstep.fetch(), plumedextras=self.plumedextras.fetch(), - init_file=self.file.fetch(), + init_file=self.file.fetch(), )