temporarily enable and disable --unsafe-fixes

dpti/equi.py

@@ -44,19 +44,19 @@
     ret += "variable        THERMO_FREQ     equal %d\n" % thermo_freq
     ret += "variable        DUMP_FREQ       equal %d\n" % dump_freq
     ret += "variable        NREPEAT         equal ${NSTEPS}/${DUMP_FREQ}\n"
-    ret += "variable        TEMP            equal %.6f\n" % temp
+    ret += f"variable        TEMP            equal {temp:.6f}\n"
     # if equi_settings['pres'] is not None :
     if pres is not None:
-        ret += "variable        PRES            equal %.6f\n" % pres
-    ret += "variable        TAU_T           equal %.6f\n" % tau_t
-    ret += "variable        TAU_P           equal %.6f\n" % tau_p
+        ret += f"variable        PRES            equal {pres:.6f}\n"
+    ret += f"variable        TAU_T           equal {tau_t:.6f}\n"
+    ret += f"variable        TAU_P           equal {tau_p:.6f}\n"
     ret += "# ---------------------- INITIALIZAITION ------------------\n"
     ret += "units           metal\n"
     ret += "boundary        p p p\n"
     ret += "atom_style      atomic\n"
     ret += "# --------------------- ATOM DEFINITION ------------------\n"
     ret += "box             tilt large\n"
-    ret += "read_data       %s\n" % equi_conf
+    ret += f"read_data       {equi_conf}\n"
     ret += "change_box      all triclinic\n"
     for jj in range(len(mass_map)):
         ret += "mass            %d %.6f\n" % (jj + 1, mass_map[jj])
@@ -82,7 +82,7 @@
     ret = ""
     ret += "# --------------------- FORCE FIELDS ---------------------\n"
     if not if_meam:
-        ret += "pair_style      deepmd %s\n" % model
+        ret += f"pair_style      deepmd {model}\n"
         ret += "pair_coeff * *\n"
     else:
         meam_library = meam_model["library"]
@@ -97,7 +97,7 @@
     ret = ""
     ret += "# --------------------- MD SETTINGS ----------------------\n"
     ret += "neighbor        1.0 bin\n"
-    ret += "timestep        %.6f\n" % timestep
+    ret += f"timestep        {timestep:.6f}\n"
     ret += "thermo          ${THERMO_FREQ}\n"
     ret += "compute         allmsd all msd\n"
     ret += "thermo_style    custom step ke pe etotal enthalpy temp press vol lx ly lz xy xz yz pxx pyy pzz pxy pxz pyz c_allmsd[*]\n"
@@ -132,7 +132,7 @@
     elif ens == "nve":
         ret += "fix             1 all nve\n"
     else:
-        raise RuntimeError("unknow ensemble %s\n" % ens)
+        raise RuntimeError(f"unknow ensemble {ens}\n")
     ret += "fix             mzero all momentum 10 linear 1 1 1\n"
     ret += "# --------------------- INITIALIZE -----------------------\n"
     ret += "velocity        all create ${TEMP} %d\n" % (

dpti/hti.py

@@ -43,7 +43,7 @@
     # sigma_hh = sparam['sigma_hh']
     activation = sparam["activation"]
     ret = ""
-    ret += "variable        EPSILON equal %f\n" % epsilon
+    ret += f"variable        EPSILON equal {epsilon:f}\n"
     ret += f"pair_style      lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
 
     element_num = sparam.get("element_num", 1)
@@ -79,7 +79,7 @@
     # sigma_hh = sparam['sigma_hh']
     activation = sparam["activation"]
     ret = ""
-    ret += "variable        EPSILON equal %f\n" % epsilon
+    ret += f"variable        EPSILON equal {epsilon:f}\n"
     ret += "variable        ONE equal 1\n"
     # if if_meam:
     #     ret += 'pair_style      hybrid/overlay meam lj/cut/soft %f %f %f  \n' % (nn, alpha_lj, rcut)
@@ -166,7 +166,7 @@
     # sigma_hh = sparam['sigma_hh']
     activation = sparam["activation"]
     ret = ""
-    ret += "variable        EPSILON equal %f\n" % epsilon
+    ret += f"variable        EPSILON equal {epsilon:f}\n"
     ret += "variable        INV_EPSILON equal -${EPSILON}\n"
     # if if_meam:
     #     ret += 'pair_style      hybrid/overlay meam lj/cut/soft %f %f %f  \n'  % (nn, alpha_lj, rcut)
@@ -248,7 +248,7 @@
     sum_str = "f_l_spring_1"
     for ii in range(1, ntypes):
         sum_str += "+f_l_spring_%s" % (ii + 1)
-    ret += "variable        l_spring equal %s\n" % (sum_str)
+    ret += f"variable        l_spring equal {sum_str}\n"
     return ret
 
 
@@ -277,7 +277,7 @@
 def _ff_two_steps(lamb, model, m_spring_k, step):
     ret = ""
     ret += "# --------------------- FORCE FIELDS ---------------------\n"
-    ret += "pair_style      deepmd %s\n" % model
+    ret += f"pair_style      deepmd {model}\n"
     ret += "pair_coeff * *\n"
 
     if step == "both" or step == "spring_off":
@@ -330,19 +330,19 @@
     ret += "variable        NSTEPS          equal %d\n" % nsteps
     ret += "variable        THERMO_FREQ     equal %d\n" % thermo_freq
     ret += "variable        DUMP_FREQ       equal %d\n" % dump_freq
-    ret += "variable        TEMP            equal %f\n" % temp
-    ret += "variable        PRES            equal %f\n" % pres
-    ret += "variable        TAU_T           equal %f\n" % tau_t
-    ret += "variable        TAU_P           equal %f\n" % tau_p
-    ret += "variable        LAMBDA          equal %.10e\n" % lamb
+    ret += f"variable        TEMP            equal {temp:f}\n"
+    ret += f"variable        PRES            equal {pres:f}\n"
+    ret += f"variable        TAU_T           equal {tau_t:f}\n"
+    ret += f"variable        TAU_P           equal {tau_p:f}\n"
+    ret += f"variable        LAMBDA          equal {lamb:.10e}\n"
     ret += "variable        INV_LAMBDA      equal %.10e\n" % (1 - lamb)
     ret += "# ---------------------- INITIALIZAITION ------------------\n"
     ret += "units           metal\n"
     ret += "boundary        p p p\n"
     ret += "atom_style      atomic\n"
     ret += "# --------------------- ATOM DEFINITION ------------------\n"
     ret += "box             tilt large\n"
-    ret += "read_data       %s\n" % conf_file
+    ret += f"read_data       {conf_file}\n"
     if copies is not None:
         ret += "replicate       %d %d %d\n" % (copies[0], copies[1], copies[2])
     ret += "change_box      all triclinic\n"
@@ -367,7 +367,7 @@
 
     ret += "# --------------------- MD SETTINGS ----------------------\n"
     ret += "neighbor        1.0 bin\n"
-    ret += "timestep        %s\n" % timestep
+    ret += f"timestep        {timestep}\n"
     ret += "thermo          ${THERMO_FREQ}\n"
     ret += "compute         allmsd all msd\n"
     if 1 - lamb != 0:
@@ -405,7 +405,7 @@
     elif ens == "nve":
         ret += "fix             1 all nve\n"
     else:
-        raise RuntimeError("unknow ensemble %s\n" % ens)
+        raise RuntimeError(f"unknow ensemble {ens}\n")
     ret += "# --------------------- INITIALIZE -----------------------\n"
     ret += "velocity        all create ${TEMP} %d\n" % (
         np.random.default_rng().integers(1, 2**16)
@@ -806,7 +806,7 @@
     from_ti = os.path.join(from_task, "hti.out")
     if not os.path.isfile(from_ti):
         raise RuntimeError(
-            "cannot find file %s, task should be computed befor refined" % from_ti
+            f"cannot find file {from_ti}, task should be computed befor refined"
         )
     tmp_array = np.loadtxt(from_ti)
     all_t = tmp_array[:, 0]
@@ -1276,9 +1276,9 @@
     info = thermo_info.copy()
 
     if jdata["reference"] == "einstein":
-        print("# free ener of Einstein Mole: %20.8f" % e0)
+        print(f"# free ener of Einstein Mole: {e0:20.8f}")
     else:
-        print("# free ener of ideal gas: %20.8f" % e0)
+        print(f"# free ener of ideal gas: {e0:20.8f}")
 
     print(
         ("# fe contrib due to integration " + print_format) % (de, de_err[0], de_err[1])

dpti/hti_ice.py

@@ -223,14 +223,14 @@
     print_format = "%20.12f  %10.3e  %10.3e"
     hti.print_thermo_info(thermo_info)
     if crystal == "vega":
-        print("# free ener of Einstein Mole: %20.8f" % (e0))
+        print(f"# free ener of Einstein Mole: {e0:20.8f}")
     else:
-        print("# free ener of Einstein Crys: %20.8f" % (e0))
+        print(f"# free ener of Einstein Crys: {e0:20.8f}")
     print(f"# Pauling corr {note_pauling}:        {pauling_corr:20.8f}")
     print(
         ("# fe integration              " + print_format) % (de, de_err[0], de_err[1])
     )
-    print("# fe const shift              %20.12f" % args.shift)
+    print(f"# fe const shift              {args.shift:20.12f}")
     # if args.type == 'helmholtz' :
     print("# Helmholtz free ener per mol (stat_err inte_err) [eV]:")
     print(print_format % (e0 + de - args.shift, de_err[0], de_err[1]))

dpti/hti_liq.py

@@ -36,7 +36,7 @@
     # sigma = sparam['sigma']
     activation = sparam["activation"]
     ret = ""
-    ret += "variable        EPSILON equal %f\n" % epsilon
+    ret += f"variable        EPSILON equal {epsilon:f}\n"
     ret += f"pair_style      lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
 
     element_num = sparam.get("element_num", 1)
@@ -66,7 +66,7 @@
     # sigma = sparam['sigma']
     activation = sparam["activation"]
     ret = ""
-    ret += "variable        EPSILON equal %f\n" % epsilon
+    ret += f"variable        EPSILON equal {epsilon:f}\n"
     ret += "variable        ONE equal 1\n"
     if if_meam:
         ret += f"pair_style      hybrid/overlay meam lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
@@ -110,7 +110,7 @@
     activation = sparam["activation"]
     ret = ""
     ret += "variable        INV_LAMBDA equal 1-${LAMBDA}\n"
-    ret += "variable        EPSILON equal %f\n" % epsilon
+    ret += f"variable        EPSILON equal {epsilon:f}\n"
     ret += "variable        INV_EPSILON equal -${EPSILON}\n"
     if if_meam:
         ret += f"pair_style      hybrid/overlay meam lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}\n"
@@ -166,19 +166,19 @@
     ret += "variable        NSTEPS          equal %d\n" % nsteps
     ret += "variable        THERMO_FREQ     equal %d\n" % thermo_freq
     ret += "variable        DUMP_FREQ       equal %d\n" % dump_freq
-    ret += "variable        TEMP            equal %f\n" % temp
-    ret += "variable        PRES            equal %f\n" % pres
-    ret += "variable        TAU_T           equal %f\n" % tau_t
-    ret += "variable        TAU_P           equal %f\n" % tau_p
-    ret += "variable        LAMBDA          equal %.10e\n" % lamb
+    ret += f"variable        TEMP            equal {temp:f}\n"
+    ret += f"variable        PRES            equal {pres:f}\n"
+    ret += f"variable        TAU_T           equal {tau_t:f}\n"
+    ret += f"variable        TAU_P           equal {tau_p:f}\n"
+    ret += f"variable        LAMBDA          equal {lamb:.10e}\n"
     ret += "variable        ZERO            equal 0\n"
     ret += "# ---------------------- INITIALIZAITION ------------------\n"
     ret += "units           metal\n"
     ret += "boundary        p p p\n"
     ret += "atom_style      atomic\n"
     ret += "# --------------------- ATOM DEFINITION ------------------\n"
     ret += "box             tilt large\n"
-    ret += "read_data       %s\n" % conf_file
+    ret += f"read_data       {conf_file}\n"
     if copies is not None:
         ret += "replicate       %d %d %d\n" % (copies[0], copies[1], copies[2])
     ret += "change_box      all triclinic\n"
@@ -199,7 +199,7 @@
         raise RuntimeError("unknown step")
     ret += "# --------------------- MD SETTINGS ----------------------\n"
     ret += "neighbor        1.0 bin\n"
-    ret += "timestep        %s\n" % timestep
+    ret += f"timestep        {timestep}\n"
     ret += "compute         allmsd all msd\n"
     ret += "thermo          ${THERMO_FREQ}\n"
     ret += "thermo_style    custom step ke pe etotal enthalpy temp press vol c_e_diff[1] c_allmsd[*]\n"
@@ -212,7 +212,7 @@
     elif ens == "nve":
         ret += "fix             1 all nve\n"
     else:
-        raise RuntimeError("unknow ensemble %s\n" % ens)
+        raise RuntimeError(f"unknow ensemble {ens}\n")
     ret += "fix             mzero all momentum 10 linear 1 1 1\n"
     ret += "# --------------------- INITIALIZE -----------------------\n"
     ret += "velocity        all create ${TEMP} %d\n" % (

dpti/hti_water.py

@@ -40,16 +40,16 @@
     sigma_hh = sparam["sigma_hh"]
     activation = sparam["activation"]
     ret = ""
-    ret += "variable        EPSILON equal %f\n" % epsilon
+    ret += f"variable        EPSILON equal {epsilon:f}\n"
     ret += f"pair_style      lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}  \n"
     ret += f"pair_coeff      1 1 ${{EPSILON}} {sigma_oo:f} {activation:f}\n"
     ret += f"pair_coeff      1 2 ${{EPSILON}} {sigma_oh:f} {activation:f}\n"
     ret += f"pair_coeff      2 2 ${{EPSILON}} {sigma_hh:f} {activation:f}\n"
     ret += "bond_style      harmonic\n"
     ret += f"bond_coeff      1 {bond_k:f} {bond_l:f}\n"
-    ret += "variable        ANGLE_K equal ${LAMBDA}*%.16e\n" % angle_k
+    ret += f"variable        ANGLE_K equal ${{LAMBDA}}*{angle_k:.16e}\n"
     ret += "angle_style     harmonic\n"
-    ret += "angle_coeff     1 ${ANGLE_K} %f\n" % (angle_t)
+    ret += f"angle_coeff     1 ${{ANGLE_K}} {angle_t:f}\n"
     ret += "fix             tot_pot all adapt/fep 0 pair lj/cut/soft epsilon * * v_LAMBDA scale yes\n"
     ret += "compute         e_diff all fep ${TEMP} pair lj/cut/soft epsilon * * v_EPSILON\n"
     return ret
@@ -69,7 +69,7 @@
     sigma_hh = sparam["sigma_hh"]
     activation = sparam["activation"]
     ret = ""
-    ret += "variable        EPSILON equal %f\n" % epsilon
+    ret += f"variable        EPSILON equal {epsilon:f}\n"
     ret += "variable        ONE equal 1\n"
     ret += f"pair_style      hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}  \n"
     ret += "pair_coeff      * * deepmd\n"
@@ -100,7 +100,7 @@
     activation = sparam["activation"]
     ret = ""
     ret += "variable        INV_LAMBDA equal 1-${LAMBDA}\n"
-    ret += "variable        EPSILON equal %f\n" % epsilon
+    ret += f"variable        EPSILON equal {epsilon:f}\n"
     ret += "variable        INV_EPSILON equal -${EPSILON}\n"
     ret += f"pair_style      hybrid/overlay deepmd {model} lj/cut/soft {nn:f} {alpha_lj:f} {rcut:f}  \n"
     ret += "pair_coeff      * * deepmd\n"
@@ -109,10 +109,10 @@
     ret += f"pair_coeff      2 2 lj/cut/soft ${{EPSILON}} {sigma_hh:f} {activation:f}\n"
     ret += "variable        BOND_K equal %.16e\n" % (bond_k * (1 - lamb))
     ret += "bond_style      harmonic\n"
-    ret += "bond_coeff      1 ${BOND_K} %f\n" % (bond_l)
+    ret += f"bond_coeff      1 ${{BOND_K}} {bond_l:f}\n"
     ret += "variable        ANGLE_K equal %.16e\n" % (angle_k * (1 - lamb))
     ret += "angle_style     harmonic\n"
-    ret += "angle_coeff     1 ${ANGLE_K} %f\n" % (angle_t)
+    ret += f"angle_coeff     1 ${{ANGLE_K}} {angle_t:f}\n"
     ret += "fix             tot_pot all adapt/fep 0 pair lj/cut/soft epsilon * * v_INV_LAMBDA scale yes\n"
     ret += "compute         e_diff all fep ${TEMP} pair lj/cut/soft epsilon * * v_INV_EPSILON\n"
     return ret
@@ -143,18 +143,18 @@
     ret += "variable        NSTEPS          equal %d\n" % nsteps
     ret += "variable        THERMO_FREQ     equal %d\n" % prt_freq
     ret += "variable        DUMP_FREQ       equal %d\n" % dump_freq
-    ret += "variable        TEMP            equal %f\n" % temp
-    ret += "variable        PRES            equal %f\n" % pres
-    ret += "variable        TAU_T           equal %f\n" % tau_t
-    ret += "variable        TAU_P           equal %f\n" % tau_p
-    ret += "variable        LAMBDA          equal %.10e\n" % lamb
+    ret += f"variable        TEMP            equal {temp:f}\n"
+    ret += f"variable        PRES            equal {pres:f}\n"
+    ret += f"variable        TAU_T           equal {tau_t:f}\n"
+    ret += f"variable        TAU_P           equal {tau_p:f}\n"
+    ret += f"variable        LAMBDA          equal {lamb:.10e}\n"
     ret += "# ---------------------- INITIALIZAITION ------------------\n"
     ret += "units           metal\n"
     ret += "boundary        p p p\n"
     ret += "atom_style      angle\n"
     ret += "# --------------------- ATOM DEFINITION ------------------\n"
     ret += "box             tilt large\n"
-    ret += "read_data       %s\n" % conf_file
+    ret += f"read_data       {conf_file}\n"
     if copies is not None:
         ret += "replicate       %d %d %d\n" % (copies[0], copies[1], copies[2])
     ret += "change_box      all triclinic\n"
@@ -170,7 +170,7 @@
     ret += "special_bonds   lj/coul 1 1 1 angle no\n"
     ret += "# --------------------- MD SETTINGS ----------------------\n"
     ret += "neighbor        1.0 bin\n"
-    ret += "timestep        %s\n" % dt
+    ret += f"timestep        {dt}\n"
     ret += "thermo          ${THERMO_FREQ}\n"
     ret += "thermo_style    custom step ke pe etotal enthalpy temp press vol ebond eangle c_e_diff[1]\n"
     ret += "thermo_modify   format 9 %.16e\n"
@@ -184,7 +184,7 @@
     elif ens == "nve":
         ret += "fix             1 all nve\n"
     else:
-        raise RuntimeError("unknow ensemble %s\n" % ens)
+        raise RuntimeError(f"unknow ensemble {ens}\n")
     ret += "fix             mzero all momentum 10 linear 1 1 1\n"
     ret += "# --------------------- INITIALIZE -----------------------\n"
     ret += "velocity        all create ${TEMP} %d\n" % (
@@ -291,7 +291,7 @@
     from_ti = os.path.join(from_task, "hti.out")
     if not os.path.isfile(from_ti):
         raise RuntimeError(
-            "cannot find file %s, task should be computed befor refined" % from_ti
+            f"cannot find file {from_ti}, task should be computed befor refined"
         )
     tmp_array = np.loadtxt(from_ti)
     all_t = tmp_array[:, 0]
@@ -667,7 +667,7 @@
 def post_tasks(iter_name, natoms, method="inte", scheme="s"):
     subtask_name = os.path.join(iter_name, "00.angle_on")
     fe = compute_ideal_mol(subtask_name)
-    print("# fe of ideal mol: %20.12f" % fe)
+    print(f"# fe of ideal mol: {fe:20.12f}")
     #    print('# fe of ideal gas: %20.12f' % (einstein.ideal_gas_fe(subtask_name) * 3))
     if method == "inte":
         e0, err0, tinfo0 = _post_tasks(subtask_name, "angle_on", natoms, scheme=scheme)