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Signed-off-by: Jinzhe Zeng <[email protected]>
njzjz · Oct 28, 2024 · 33a54c2 · 33a54c2
1 parent c38460f
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Showing 10 changed files with 44 additions and 44 deletions.
diff --git a/deepmd/tf/nvnmd/entrypoints/wrap.py b/deepmd/tf/nvnmd/entrypoints/wrap.py
@@ -116,16 +116,16 @@ def wrap(self):
         # extend data according to the number of bits per row of BRAM
         nbit = 32
         if nvnmd_cfg.version == 0:
-            data = [hcfg, hfps, hbps, hswt, hdsw, hfea, hgra]
+            datas = [hcfg, hfps, hbps, hswt, hdsw, hfea, hgra]
             keys = "cfg fps bps swt dsw fea gra".split()
         if nvnmd_cfg.version == 1:
             keys = "cfg fps bps swt dsw std fea gra gtt avc".split()
-            data = [hcfg, hfps, hbps, hswt, hdsw, hstd, hfea, hgra, hgtt, havc]
+            datas = [hcfg, hfps, hbps, hswt, hdsw, hstd, hfea, hgra, hgtt, havc]
         nhs = []
         nws = []
-        for ii in range(len(data)):
+        for ii in range(len(datas)):
             k = keys[ii]
-            d = data[ii]
+            d = datas[ii]
             h = len(d)
             w = len(d[0])  # nhex
             w4 = w * 4  # nbit
@@ -138,15 +138,15 @@ def wrap(self):
             if jdata_sys["debug"]:
                 log.info("%s: %d x % d bit" % (k, h, w * 4))
                 FioTxt().save(f"nvnmd/wrap/h{k}.txt", d)
-            data[ii] = d
+            datas[ii] = d
         # update h & w of nvnmd_cfg
         nvnmd_cfg.size["NH_DATA"] = nhs
         nvnmd_cfg.size["NW_DATA"] = nws
         nvnmd_cfg.save(nvnmd_cfg.config_file)
         head = self.wrap_head(nhs, nws)
         # output model
         hs = [*head]
-        for d in data:
+        for d in datas:
             hs.extend(d)
 
         FioBin().save(self.model_file, hs)

diff --git a/doc/model/dplr.md b/doc/model/dplr.md
@@ -168,7 +168,7 @@ pair_style      deepmd ener.pb
 pair_coeff      * *
 bond_style      zero
 bond_coeff      *
-special_bonds   lj/could 1 1 1 angle no
+special_bonds   lj/coul 1 1 1 angle no
 ```
 
 Type 1 and 2 (O and H) are `real_atom`s, while type 3 (WCs) are `virtual_atom`s. The model file `ener.pb` stores both the DW and DPLR models, so the position of WCs and the energy can be inferred from it. A virtual bond type is specified by `bond_style zero`. The `special_bonds` command switches off the exclusion of intramolecular interactions.

diff --git a/examples/data_conv/OUTCAR b/examples/data_conv/OUTCAR
@@ -39,7 +39,7 @@
    LEXCH  = PE
    EATOM  =   432.3788 eV,   31.7789 Ry
 
-   TITLE  = PAW_PBE O_h 06Feb2004
+   TITEL  = PAW_PBE O_h 06Feb2004
    LULTRA =        F    use ultrasoft PP ?
    IUNSCR =        1    unscreen: 0-lin 1-nonlin 2-no
    RPACOR =    0.800    partial core radius
@@ -93,7 +93,7 @@
    LEXCH  = PE
    EATOM  =    12.4884 eV,    0.9179 Ry
 
-   TITLE  = PAW_PBE H_h 06Feb2004
+   TITEL  = PAW_PBE H_h 06Feb2004
    LULTRA =        F    use ultrasoft PP ?
    IUNSCR =        0    unscreen: 0-lin 1-nonlin 2-no
    RPACOR =    0.000    partial core radius
@@ -297,8 +297,8 @@ Space group operators:
 
  Intra band minimization:
    WEIMIN = 0.0000     energy-eigenvalue tresh-hold
-   EBREAK =  0.16E-09  absolute break condition
-   DEPER  =   0.30     relative break condition
+   EBREAK =  0.16E-09  absolut break condition
+   DEPER  =   0.30     relativ break condition
 
    TIME   =   0.40     timestep for ELM
 
@@ -339,7 +339,7 @@ Space group operators:
    KINTER  =     0    interpolate to denser k-point grid
    CSHIFT  =0.1000    complex shift for real part using Kramers Kronig
    OMEGAMAX=  -1.0    maximum frequency
-   DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degenerate
+   DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate
    RTIME   =   -0.100 relaxation time in fs
   (WPLASMAI=    0.000 imaginary part of plasma frequency in eV, 0.658/RTIME)
    DFIELD  = 0.0000000 0.0000000 0.0000000 field for delta impulse in time
@@ -2475,7 +2475,7 @@ Space group operators:
 
 
 
- General timing and accounting information for this job:
+ General timing and accounting informations for this job:
  ========================================================
 
                   Total CPU time used (sec):      877.816

diff --git a/examples/water/dplr/lmp/in.lammps b/examples/water/dplr/lmp/in.lammps
@@ -6,7 +6,7 @@ variable	KMESH		equal 32
 variable        THERMO_FREQ     equal 2
 variable        DUMP_FREQ       equal 20
 variable        TEMP            equal 300.000000
-variable        PRESS            equal 1.000000
+variable        PRES            equal 1.000000
 variable        TAU_T           equal 0.100000
 variable        TAU_P           equal 0.500000
 
@@ -33,7 +33,7 @@ pair_style	deepmd ener.pb
 pair_coeff	* *
 bond_style	zero
 bond_coeff	*
-special_bonds   lj/could 1 1 1 angle no
+special_bonds   lj/coul 1 1 1 angle no
 
 # kspace_style "pppm/dplr" should be used. in addition the
 # gewald(1/distance) should be set the same as that used in

diff --git a/source/lmp/tests/test_dplr.py b/source/lmp/tests/test_dplr.py
@@ -384,7 +384,7 @@ def test_pair_deepmd_lr(lammps):
     lammps.pair_coeff("* *")
     lammps.bond_style("zero")
     lammps.bond_coeff("*")
-    lammps.special_bonds("lj/could 1 1 1 angle no")
+    lammps.special_bonds("lj/coul 1 1 1 angle no")
     lammps.kspace_style("pppm/dplr 1e-5")
     lammps.kspace_modify(f"gewald {beta:.2f} diff ik mesh {mesh:d} {mesh:d} {mesh:d}")
     lammps.fix(f"0 all dplr model {pb_file.resolve()} type_associate 1 3 bond_type 1")
@@ -410,7 +410,7 @@ def test_pair_deepmd_lr_efield_constant(lammps):
     lammps.pair_coeff("* *")
     lammps.bond_style("zero")
     lammps.bond_coeff("*")
-    lammps.special_bonds("lj/could 1 1 1 angle no")
+    lammps.special_bonds("lj/coul 1 1 1 angle no")
     lammps.fix(
         f"0 all dplr model {pb_file.resolve()} type_associate 1 3 bond_type 1 efield 0 0 1"
     )
@@ -446,7 +446,7 @@ def test_pair_deepmd_lr_efield_variable(lammps):
     lammps.pair_coeff("* *")
     lammps.bond_style("zero")
     lammps.bond_coeff("*")
-    lammps.special_bonds("lj/could 1 1 1 angle no")
+    lammps.special_bonds("lj/coul 1 1 1 angle no")
     lammps.fix(
         f"0 all dplr model {pb_file.resolve()} type_associate 1 3 bond_type 1 efield 0 0 v_EFIELD_Z"
     )
@@ -481,7 +481,7 @@ def test_min_dplr(lammps):
     lammps.pair_coeff("* *")
     lammps.bond_style("zero")
     lammps.bond_coeff("*")
-    lammps.special_bonds("lj/could 1 1 1 angle no")
+    lammps.special_bonds("lj/coul 1 1 1 angle no")
     lammps.kspace_style("pppm/dplr 1e-5")
     lammps.kspace_modify(f"gewald {beta:.2f} diff ik mesh {mesh:d} {mesh:d} {mesh:d}")
     lammps.fix(f"0 all dplr model {pb_file.resolve()} type_associate 1 3 bond_type 1")
@@ -505,7 +505,7 @@ def test_pair_deepmd_lr_type_map(lammps_type_map):
     lammps_type_map.pair_coeff("* * H O")
     lammps_type_map.bond_style("zero")
     lammps_type_map.bond_coeff("*")
-    lammps_type_map.special_bonds("lj/could 1 1 1 angle no")
+    lammps_type_map.special_bonds("lj/coul 1 1 1 angle no")
     lammps_type_map.kspace_style("pppm/dplr 1e-5")
     lammps_type_map.kspace_modify(
         f"gewald {beta:.2f} diff ik mesh {mesh:d} {mesh:d} {mesh:d}"
@@ -535,7 +535,7 @@ def test_pair_deepmd_lr_si(lammps_si):
     lammps_si.pair_coeff("* *")
     lammps_si.bond_style("zero")
     lammps_si.bond_coeff("*")
-    lammps_si.special_bonds("lj/could 1 1 1 angle no")
+    lammps_si.special_bonds("lj/coul 1 1 1 angle no")
     lammps_si.kspace_style("pppm/dplr 1e-5")
     lammps_si.kspace_modify(
         f"gewald {beta / constants.dist_metal2si:.6e} diff ik mesh {mesh:d} {mesh:d} {mesh:d}"

diff --git a/source/tests/pt/model/test_dpa1.py b/source/tests/pt/model/test_dpa1.py
@@ -42,7 +42,7 @@ def test_consistency(
         dstd = rng.normal(size=(self.nt, nnei, 4))
         dstd = 0.1 + np.abs(dstd)
 
-        for idt, sm, to, tm, prec, etc in itertools.product(
+        for idt, sm, to, tm, prec, ect in itertools.product(
             [False, True],  # resnet_dt
             [False, True],  # smooth_type_embedding
             [False, True],  # type_one_side
@@ -68,8 +68,8 @@ def test_consistency(
                 smooth_type_embedding=sm,
                 type_one_side=to,
                 tebd_input_mode=tm,
-                use_econf_tebd=etc,
-                type_map=["O", "H"] if etc else None,
+                use_econf_tebd=ect,
+                type_map=["O", "H"] if ect else None,
                 seed=GLOBAL_SEED,
             ).to(env.DEVICE)
             dd0.se_atten.mean = torch.tensor(davg, dtype=dtype, device=env.DEVICE)
@@ -117,7 +117,7 @@ def test_jit(
         dstd = rng.normal(size=(self.nt, nnei, 4))
         dstd = 0.1 + np.abs(dstd)
 
-        for idt, prec, sm, to, tm, etc in itertools.product(
+        for idt, prec, sm, to, tm, ect in itertools.product(
             [
                 False,
             ],  # resnet_dt
@@ -145,8 +145,8 @@ def test_jit(
                 smooth_type_embedding=sm,
                 type_one_side=to,
                 tebd_input_mode=tm,
-                use_econf_tebd=etc,
-                type_map=["O", "H"] if etc else None,
+                use_econf_tebd=ect,
+                type_map=["O", "H"] if ect else None,
                 seed=GLOBAL_SEED,
             )
             dd0.se_atten.mean = torch.tensor(davg, dtype=dtype, device=env.DEVICE)

diff --git a/source/tests/pt/model/test_se_atten_v2.py b/source/tests/pt/model/test_se_atten_v2.py
@@ -42,7 +42,7 @@ def test_consistency(
         dstd = rng.normal(size=(self.nt, nnei, 4))
         dstd = 0.1 + np.abs(dstd)
 
-        for idt, to, prec, etc in itertools.product(
+        for idt, to, prec, ect in itertools.product(
             [False, True],  # resnet_dt
             [False, True],  # type_one_side
             [
@@ -64,8 +64,8 @@ def test_consistency(
                 precision=prec,
                 resnet_dt=idt,
                 type_one_side=to,
-                use_econf_tebd=etc,
-                type_map=["O", "H"] if etc else None,
+                use_econf_tebd=ect,
+                type_map=["O", "H"] if ect else None,
                 seed=GLOBAL_SEED,
             ).to(env.DEVICE)
             dd0.se_atten.mean = torch.tensor(davg, dtype=dtype, device=env.DEVICE)
@@ -113,7 +113,7 @@ def test_jit(
         dstd = rng.normal(size=(self.nt, nnei, 4))
         dstd = 0.1 + np.abs(dstd)
 
-        for idt, prec, to, etc in itertools.product(
+        for idt, prec, to, ect in itertools.product(
             [
                 False,
             ],  # resnet_dt
@@ -135,8 +135,8 @@ def test_jit(
                 precision=prec,
                 resnet_dt=idt,
                 type_one_side=to,
-                use_econf_tebd=etc,
-                type_map=["O", "H"] if etc else None,
+                use_econf_tebd=ect,
+                type_map=["O", "H"] if ect else None,
                 seed=GLOBAL_SEED,
             )
             dd0.se_atten.mean = torch.tensor(davg, dtype=dtype, device=env.DEVICE)

diff --git a/source/tests/tf/test_data_large_batch.py b/source/tests/tf/test_data_large_batch.py
@@ -186,7 +186,7 @@ def test_data_mixed_type(self):
         sess.run(tf.global_variables_initializer())
         [e, f, v] = sess.run([energy, force, virial], feed_dict=feed_dict_test)
         # print(sess.run(model.type_embedding))
-        # np.savetxt('tmp.out', sess.run(descrpt.doubt, feed_dict = feed_dict_test), fmt='%.10e')
+        # np.savetxt('tmp.out', sess.run(descrpt.dout, feed_dict = feed_dict_test), fmt='%.10e')
         # # print(sess.run(model.atype_embed, feed_dict = feed_dict_test))
         # print(sess.run(fitting.inputs, feed_dict = feed_dict_test))
         # print(sess.run(fitting.outs, feed_dict = feed_dict_test))
@@ -386,7 +386,7 @@ def test_stripped_data_mixed_type(self):
         sess.run(tf.global_variables_initializer())
         [e, f, v] = sess.run([energy, force, virial], feed_dict=feed_dict_test)
         # print(sess.run(model.type_embedding))
-        # np.savetxt('tmp.out', sess.run(descrpt.doubt, feed_dict = feed_dict_test), fmt='%.10e')
+        # np.savetxt('tmp.out', sess.run(descrpt.dout, feed_dict = feed_dict_test), fmt='%.10e')
         # # print(sess.run(model.atype_embed, feed_dict = feed_dict_test))
         # print(sess.run(fitting.inputs, feed_dict = feed_dict_test))
         # print(sess.run(fitting.outs, feed_dict = feed_dict_test))
@@ -586,7 +586,7 @@ def test_compressible_data_mixed_type(self):
         sess.run(tf.global_variables_initializer())
         [e, f, v] = sess.run([energy, force, virial], feed_dict=feed_dict_test)
         # print(sess.run(model.type_embedding))
-        # np.savetxt('tmp.out', sess.run(descrpt.doubt, feed_dict = feed_dict_test), fmt='%.10e')
+        # np.savetxt('tmp.out', sess.run(descrpt.dout, feed_dict = feed_dict_test), fmt='%.10e')
         # # print(sess.run(model.atype_embed, feed_dict = feed_dict_test))
         # print(sess.run(fitting.inputs, feed_dict = feed_dict_test))
         # print(sess.run(fitting.outs, feed_dict = feed_dict_test))

diff --git a/source/tests/tf/test_descrpt_hybrid.py b/source/tests/tf/test_descrpt_hybrid.py
@@ -88,7 +88,7 @@ def test_descriptor_hybrid(self):
 
         type_embedding = typeebd.build(ntypes, suffix="_hybrid")
 
-        doubt = descrpt.build(
+        dout = descrpt.build(
             t_coord,
             t_type,
             t_natoms,
@@ -115,7 +115,7 @@ def test_descriptor_hybrid(self):
 
         sess = self.cached_session().__enter__()
         sess.run(tf.global_variables_initializer())
-        [model_dout] = sess.run([doubt], feed_dict=feed_dict_test)
+        [model_dout] = sess.run([dout], feed_dict=feed_dict_test)
 
         ref_dout1 = [
             1.34439289e-03,

diff --git a/source/tests/tf/test_type_one_side.py b/source/tests/tf/test_type_one_side.py
@@ -69,7 +69,7 @@ def test_descriptor_one_side_exclude_types(self):
 
         # successful
         descrpt = Descriptor(**jdata["model"]["descriptor"])
-        doubt = descrpt.build(
+        dout = descrpt.build(
             t_coord,
             t_type,
             t_natoms,
@@ -125,8 +125,8 @@ def test_descriptor_one_side_exclude_types(self):
 
         with self.cached_session() as sess:
             sess.run(tf.global_variables_initializer())
-            [model_dout1] = sess.run([doubt], feed_dict=feed_dict_test1)
-            [model_dout2] = sess.run([doubt], feed_dict=feed_dict_test2)
+            [model_dout1] = sess.run([dout], feed_dict=feed_dict_test1)
+            [model_dout2] = sess.run([dout], feed_dict=feed_dict_test2)
             [model_dout1_failed] = sess.run([dout_failed], feed_dict=feed_dict_test1)
             [model_dout2_failed] = sess.run([dout_failed], feed_dict=feed_dict_test2)
         model_dout1 = model_dout1.reshape([6, -1])
@@ -175,7 +175,7 @@ def test_se_r_one_side_exclude_types(self):
 
         # successful
         descrpt = Descriptor(**jdata["model"]["descriptor"])
-        doubt = descrpt.build(
+        dout = descrpt.build(
             t_coord,
             t_type,
             t_natoms,
@@ -231,8 +231,8 @@ def test_se_r_one_side_exclude_types(self):
 
         with self.cached_session() as sess:
             sess.run(tf.global_variables_initializer())
-            [model_dout1] = sess.run([doubt], feed_dict=feed_dict_test1)
-            [model_dout2] = sess.run([doubt], feed_dict=feed_dict_test2)
+            [model_dout1] = sess.run([dout], feed_dict=feed_dict_test1)
+            [model_dout2] = sess.run([dout], feed_dict=feed_dict_test2)
             [model_dout1_failed] = sess.run([dout_failed], feed_dict=feed_dict_test1)
             [model_dout2_failed] = sess.run([dout_failed], feed_dict=feed_dict_test2)
         model_dout1 = model_dout1.reshape([6, -1])