Replace &> run.log with > run.log 2>&1 (dash compatible)

src/hydration.py

@@ -210,7 +210,7 @@ def run_simulation(self, label, liq, AGrad=True):
  logger.info("You may tail -f %s/npt.out in another terminal window\n" % os.getcwd())
  _exec(cmdstr, copy_stderr=True, outfnm='md.out')
  else:
- queue_up(wq, command = cmdstr+' &> md.out', tag='%s:%s/%s' % (self.name, label, "liq" if liq else "gas"),
+ queue_up(wq, command = cmdstr+' > md.out 2>&1', tag='%s:%s/%s' % (self.name, label, "liq" if liq else "gas"),
  input_files = self.scripts + ['simulation.p', 'forcefield.p', os.path.basename(self.molecules[label])],
  output_files = ['md_result.p', 'md.out'] + self.extra_output, tgt=self, verbose=False, print_time=3600)
  os.chdir('..')

src/lipid.py

@@ -326,7 +326,7 @@ def npt_simulation(self, temperature, pressure, simnum):
  logger.info("You may tail -f %s/npt.out in another terminal window\n" % os.getcwd())
  _exec(cmdstr, copy_stderr=True, outfnm='npt.out')
  else:
- queue_up(wq, command = cmdstr+' &> npt.out',
+ queue_up(wq, command = cmdstr+' > npt.out 2>&1',
  input_files = self.nptfiles + self.scripts + ['forcebalance.p'],
  output_files = ['npt_result.p', 'npt.out'] + self.extra_output, tgt=self)
 

src/psi4io.py

@@ -381,7 +381,7 @@ def submit_psi(this_apath, dname, these_mvals):
  input_files += [(os.path.join(self.root, self.tgtdir, dname, "build.dat"), "build.dat")]
  input_files += [(os.path.join(os.path.split(__file__)[0],"data","run_psi_rdvr3_objective.sh"), "run_psi_rdvr3_objective.sh")]
  logger.info("\r")
- queue_up_src_dest(wq,"sh run_psi_rdvr3_objective.sh -c %s &> run_psi_rdvr3_objective.log" % os.path.join(self.root, self.tgtdir, dname),
+ queue_up_src_dest(wq,"sh run_psi_rdvr3_objective.sh -c %s > run_psi_rdvr3_objective.log 2>&1" % os.path.join(self.root, self.tgtdir, dname),
  input_files=input_files,
  output_files=[(os.path.join(this_apath, i),i) for i in ["run_psi_rdvr3_objective.log", "output.dat"]], verbose=False)
  os.chdir(cwd)