vasputils 0.0.10 → 0.0.11

data/test/potcar/test.vasputils

@@ -0,0 +1,307 @@
+--- # vim: syntax=yaml
+
+potcar_path: test/potcar/dummy
+element_potcar:
+  Ac:      Ac          # 11.0000000000000
+  Ag:      Ag_pv       # 17.0000000000000
+ #Al:      Al          #  3.00000000000000
+ #Al:      Al_GW       #  3.00000000000000
+  Al:      Al_sv_GW    # 11.0000000000000
+  Am:      Am          # 17.0000000000000
+ #Ar:      Ar          #  8.00000000000000
+  Ar:      Ar_GW       #  8.00000000000000
+ #As:      As          #  5.00000000000000
+ #As:      As_GW       #  5.00000000000000
+  As:      As_d        # 15.0000000000000
+ #At:      At          #  7.00000000000000
+  At:      At_d        # 17.0000000000000
+ #Au:      Au          # 11.0000000000000
+ #Au:      Au_GW       # 11.0000000000000
+  Au:      Au_pv_GW    # 17.0000000000000
+  B :      B           #  3.00000000000000
+ #B :      B_GW        #  3.00000000000000
+ #B :      B_h         #  3.00000000000000
+ #B :      B_s         #  3.00000000000000
+  Ba:      Ba_sv       # 10.0000000000000
+ #Ba:      Ba_sv_GW    # 10.0000000000000
+ #Be:      Be          #  2.00000000000000
+ #Be:      Be_GW       #  2.00000000000000
+ #Be:      Be_sv       #  4.00000000000000
+ #Be:      Be_sv_GW    #  4.00000000000000
+ #Bi:      Bi          #  5.00000000000000
+ #Bi:      Bi_GW       #  5.00000000000000
+  Bi:      Bi_d        # 15.0000000000000
+ #Bi:      Bi_d_GW     # 15.0000000000000
+  Br:      Br          #  7.00000000000000
+ #Br:      Br_GW       #  7.00000000000000
+  C :      C           #  4.00000000000000
+ #C :      C_GW        #  4.00000000000000
+ #C :      C_GW_new    #  4.00000000000000
+ #C :      C_h         #  4.00000000000000
+ #C :      C_s         #  4.00000000000000
+ #Ca:      Ca_pv       #  8.00000000000000
+  Ca:      Ca_sv       # 10.0000000000000
+ #Ca:      Ca_sv_GW    # 10.0000000000000
+ #Cd:      Cd          # 12.0000000000000
+ #Cd:      Cd_GW       # 12.0000000000000
+ #Cd:      Cd_pv_GW    # 18.0000000000000
+  Cd:      Cd_sv_GW    # 20.0000000000000
+  Ce:      Ce          # 12.0000000000000
+ #Ce:      Ce_3        # 11.0000000000000
+ #Ce:      Ce_GW       # 12.0000000000000
+ #Ce:      Ce_h        # 12.0000000000000
+  Cl:      Cl          #  7.00000000000000
+ #Cl:      Cl_GW       #  7.00000000000000
+ #Cl:      Cl_h        #  7.00000000000000
+  Cm:      Cm          # 18.0000000000000
+ #Co:      Co          #  9.00000000000000
+ #Co:      Co_GW       #  9.00000000000000
+ #Co:      Co_pv       # 15.0000000000000
+  Co:      Co_sv       # 17.0000000000000
+ #Co:      Co_sv_GW    # 17.0000000000000
+ #Cr:      Cr          #  6.00000000000000
+ #Cr:      Cr_pv       # 12.0000000000000
+  Cr:      Cr_sv       # 14.0000000000000
+ #Cr:      Cr_sv_GW    # 14.0000000000000
+  Cs:      Cs_sv       #  9.00000000000000
+ #Cs:      Cs_sv_GW    #  9.00000000000000
+ #Cu:      Cu          # 11.0000000000000
+ #Cu:      Cu_GW       # 11.0000000000000
+  Cu:      Cu_pv       # 17.0000000000000
+ #Cu:      Cu_pv_GW    # 17.0000000000000
+  Dy:      Dy          # 20.0000000000000
+ #Dy:      Dy_3        #  9.00000000000000
+  Er:      Er          # 22.0000000000000
+ #Er:      Er_2        #  8.00000000000000
+ #Er:      Er_3        #  9.00000000000000
+  Eu:      Eu          # 17.0000000000000
+ #Eu:      Eu_2        #  8.00000000000000
+ #Eu:      Eu_3        #  9.00000000000000
+  F :      F           #  7.00000000000000
+ #F :      F_GW        #  7.00000000000000
+ #F :      F_GW_new    #  7.00000000000000
+ #F :      F_h         #  7.00000000000000
+ #F :      F_s         #  7.00000000000000
+ #Fe:      Fe          #  8.00000000000000
+ #Fe:      Fe_GW       #  8.00000000000000
+ #Fe:      Fe_pv       # 14.0000000000000
+  Fe:      Fe_sv       # 16.0000000000000
+ #Fe:      Fe_sv_GW    # 16.0000000000000
+  Fr:      Fr_sv       #  9.00000000000000
+ #Ga:      Ga          #  3.00000000000000
+ #Ga:      Ga_GW       #  3.00000000000000
+ #Ga:      Ga_d        # 13.0000000000000
+ #Ga:      Ga_d_GW     # 13.0000000000000
+ #Ga:      Ga_h        # 13.0000000000000
+ #Ga:      Ga_pv_GW    # 19.0000000000000
+  Ga:      Ga_sv_GW    # 21.0000000000000
+  Gd:      Gd          # 18.0000000000000
+ #Gd:      Gd_3        #  9.00000000000000
+ #Ge:      Ge          #  4.00000000000000
+ #Ge:      Ge_GW       #  4.00000000000000
+ #Ge:      Ge_d        # 14.0000000000000
+ #Ge:      Ge_d_GW     # 14.0000000000000
+ #Ge:      Ge_h        # 14.0000000000000
+  Ge:      Ge_sv_GW    # 22.0000000000000
+ #H :     H.5          #  0.500000000000000
+ #H :     H.25         #  0.250000000000000
+ #H :     H.33         #  0.330000000000000
+ #H :     H.42         #  0.420000000000000
+ #H :     H.58         #  0.580000000000000
+ #H :     H.66         #  0.660000000000000
+ #H :     H.75         #  0.750000000000000
+  H :      H           #  1.00000000000000
+ #H :      H1.5        #  1.50000000000000
+ #H :      H1.25       #  1.25000000000000
+ #H :      H1.33       #  1.33000000000000
+ #H :      H1.66       #  1.66000000000000
+ #H :      H1.75       #  1.75000000000000
+ #H :      H_AE        #  1.0000000000000000
+ #H :      H_GW        #  1.00000000000000
+ #H :      H_h         #  1.00000000000000
+ #H :      H_h_GW      #  1.00000000000000
+ #H :      H_s         #  1.00000000000000
+  He:      He          #  2.00000000000000
+ #He:      He_GW       #  2.00000000000000
+ #Hf:      Hf          #  4.00000000000000
+ #Hf:      Hf_pv       # 10.0000000000000
+  Hf:      Hf_sv       # 12.0000000000000
+ #Hf:      Hf_sv_GW    # 12.0000000000000
+  Hg:      Hg          # 12.0000000000000
+  Ho:      Ho          # 21.0000000000000
+ #Ho:      Ho_3        #  9.00000000000000
+  I :      I           #  7.00000000000000
+ #I :      I_GW        #  7.00000000000000
+ #In:      In          #  3.00000000000000
+  In:      In_d        # 13.0000000000000
+ #In:      In_d_GW     # 13.0000000000000
+ #Ir:      Ir          #  9.00000000000000
+  Ir:      Ir_sv_GW    # 17.0000000000000
+ #K :      K_pv        #  7.00000000000000
+  K :      K_sv        #  9.00000000000000
+ #K :      K_sv_GW     #  9.00000000000000
+  Kr:      Kr          #  8.00000000000000
+ #Kr:      Kr_GW       #  8.00000000000000
+  La:      La          # 11.0000000000000
+ #La:      La_s        #  9.00000000000000
+ #Li:      Li          #  1.00000000000000
+ #Li:      Li_AE_GW    #  3.00000000000000
+ #Li:      Li_GW       #  1.00000000000000
+  Li:      Li_sv       #  3.00000000000000
+ #Li:      Li_sv_GW    #  3.00000000000000
+  Lu:      Lu          # 25.0000000000000
+ #Lu:      Lu_3        #  9.00000000000000
+ #Mg:      Mg          #  2.00000000000000
+ #Mg:      Mg_GW       #  2.00000000000000
+ #Mg:      Mg_pv       #  8.00000000000000
+ #Mg:      Mg_pv_GW    #  8.00000000000000
+  Mg:      Mg_sv       # 10.0000000000000
+ #Mg:      Mg_sv_GW    # 10.0000000000000
+ #Mn:      Mn          #  7.00000000000000
+ #Mn:      Mn_GW       #  7.00000000000000
+ #Mn:      Mn_pv       # 13.0000000000000
+  Mn:      Mn_sv       # 15.0000000000000
+ #Mn:      Mn_sv_GW    # 15.0000000000000
+ #Mo:      Mo          #  6.00000000000000
+ #Mo:      Mo_pv       # 12.0000000000000
+  Mo:      Mo_sv       # 14.0000000000000
+ #Mo:      Mo_sv_GW    # 14.0000000000000
+  N :      N           #  5.00000000000000
+ #N :      N_GW        #  5.00000000000000
+ #N :      N_GW_new    #  5.00000000000000
+ #N :      N_h         #  5.00000000000000
+ #N :      N_s         #  5.00000000000000
+ #N :      N_s_GW      #  5.00000000000000
+ #Na:      Na          #  1.00000000000000
+ #Na:      Na_pv       #  7.00000000000000
+  Na:      Na_sv       #  9.00000000000000
+ #Na:      Na_sv_GW    #  9.00000000000000
+ #Nb:      Nb_pv       # 11.0000000000000
+  Nb:      Nb_sv       # 13.0000000000000
+ #Nb:      Nb_sv_GW    # 13.0000000000000
+  Nd:      Nd          # 14.0000000000000
+ #Nd:      Nd_3        # 11.0000000000000
+  Ne:      Ne          #  8.00000000000000
+ #Ne:      Ne_GW       #  8.00000000000000
+ #Ne:      Ne_GW_soft  #  8.00000000000000
+ #Ni:      Ni          # 10.0000000000000
+ #Ni:      Ni_GW       # 10.0000000000000
+ #Ni:      Ni_pv       # 16.0000000000000
+  Ni:      Ni_sv_GW    # 18.0000000000000
+  Np:      Np          # 15.0000000000000
+ #Np:      Np_s        # 15.0000000000000
+  O :      O           #  6.00000000000000
+ #O :      O_GW        #  6.00000000000000
+ #O :      O_GW_new    #  6.00000000000000
+ #O :      O_h         #  6.00000000000000
+ #O :      O_s         #  6.00000000000000
+ #O :      O_s_GW      #  6.00000000000000
+ #Os:      Os          #  8.00000000000000
+ #Os:      Os_pv       # 14.0000000000000
+  Os:      Os_sv_GW    # 16.0000000000000
+  P :      P           #  5.00000000000000
+ #P :      P_GW        #  5.00000000000000
+ #P :      P_h         #  5.00000000000000
+  Pa:      Pa          # 13.0000000000000
+ #Pa:      Pa_s        # 11.0000000000000
+ #Pb:      Pb          #  4.00000000000000
+  Pb:      Pb_d        # 14.0000000000000
+ #Pb:      Pb_d_GW     # 14.0000000000000
+ #Pd:      Pd          # 10.0000000000000
+ #Pd:      Pd_GW       # 10.0000000000000
+  Pd:      Pd_pv       # 16.0000000000000
+  Pm:      Pm          # 15.0000000000000
+ #Pm:      Pm_3        # 11.0000000000000
+ #Po:      Po          #  6.00000000000000
+  Po:      Po_d        # 16.0000000000000
+  Pr:      Pr          # 13.0000000000000
+ #Pr:      Pr_3        # 11.0000000000000
+ #Pt:      Pt          # 10.0000000000000
+ #Pt:      Pt_GW       # 10.0000000000000
+ #Pt:      Pt_pv       # 16.0000000000000
+ #Pt:      Pt_pv_GW    # 16.0000000000000
+  Pt:      Pt_sv_GW    # 18.0000000000000
+  Pu:      Pu          # 16.0000000000000
+ #Pu:      Pu_s        # 16.0000000000000
+  Ra:      Ra_sv       # 10.0000000000000
+ #Rb:      Rb_pv       #  7.00000000000000
+  Rb:      Rb_sv       #  9.00000000000000
+ #Rb:      Rb_sv_GW    #  9.00000000000000
+ #Re:      Re          #  7.00000000000000
+ #Re:      Re_pv       # 13.0000000000000
+  Re:      Re_sv_GW    # 15.0000000000000
+ #Rh:      Rh          #  9.00000000000000
+ #Rh:      Rh_GW       #  9.00000000000000
+ #Rh:      Rh_pv       # 15.0000000000000
+ #Rh:      Rh_pv_GW    # 15.0000000000000
+  Rh:      Rh_sv_GW    # 17.0000000000000
+  Rn:      Rn          #  8.00000000000000
+ #Ru:      Ru          #  8.00000000000000
+ #Ru:      Ru_pv       # 14.0000000000000
+ #Ru:      Ru_pv_GW    # 14.0000000000000
+  Ru:      Ru_sv       # 16.0000000000000
+ #Ru:      Ru_sv_GW    # 16.0000000000000
+  S :      S           #  6.00000000000000
+ #S :      S_GW        #  6.00000000000000
+ #S :      S_h         #  6.00000000000000
+ #Sb:      Sb          #  5.00000000000000
+ #Sb:      Sb_GW       #  5.00000000000000
+  Sb:      Sb_d_GW     # 15.0000000000000
+ #Sc:      Sc          #  3.00000000000000
+  Sc:      Sc_sv       # 11.0000000000000
+ #Sc:      Sc_sv_GW    # 11.0000000000000
+  Se:      Se          #  6.00000000000000
+ #Se:      Se_GW       #  6.00000000000000
+ #Si:      Si          #  4.00000000000000
+ #Si:      Si_GW       #  4.00000000000000
+  Si:      Si_sv_GW    # 12.0000000000000
+  Sm:      Sm          # 16.0000000000000
+ #Sm:      Sm_3        # 11.0000000000000
+ #Sn:      Sn          #  4.00000000000000
+  Sn:      Sn_d        # 14.0000000000000
+ #Sn:      Sn_d_GW     # 14.0000000000000
+  Sr:      Sr_sv       # 10.0000000000000
+ #Sr:      Sr_sv_GW    # 10.0000000000000
+ #Ta:      Ta          #  5.00000000000000
+ #Ta:      Ta_pv       # 11.0000000000000
+  Ta:      Ta_sv_GW    # 13.0000000000000
+  Tb:      Tb          # 19.0000000000000
+ #Tb:      Tb_3        #  9.00000000000000
+ #Tc:      Tc          #  7.00000000000000
+ #Tc:      Tc_pv       # 13.0000000000000
+  Tc:      Tc_sv       # 15.0000000000000
+ #Tc:      Tc_sv_GW    # 15.0000000000000
+  Te:      Te          #  6.00000000000000
+ #Te:      Te_GW       #  6.00000000000000
+  Th:      Th          # 12.0000000000000
+ #Th:      Th_s        # 10.0000000000000
+ #Ti:      Ti          #  4.00000000000000
+ #Ti:      Ti_pv       # 10.0000000000000
+  Ti:      Ti_sv       # 12.0000000000000
+ #Ti:      Ti_sv_GW    # 12.0000000000000
+ #Tl:      Tl          #  3.00000000000000
+  Tl:      Tl_d        # 13.0000000000000
+  Tm:      Tm          # 23.0000000000000
+ #Tm:      Tm_3        #  9.00000000000000
+  U :      U           # 14.0000000000000
+ #U :      U_s         # 14.0000000000000
+ #V :      V           #  5.00000000000000
+ #V :      V_pv        # 11.0000000000000
+  V :      V_sv        # 13.0000000000000
+ #V :      V_sv_GW     # 13.0000000000000
+ #W :      W           #  6.00000000000000
+ #W :      W_pv        # 12.0000000000000
+  W :      W_sv_GW     # 14.0000000000000
+  Xe:      Xe          #  8.00000000000000
+ #Xe:      Xe_GW       #  8.00000000000000
+  Y :      Y_sv        # 11.0000000000000
+ #Y :      Y_sv_GW     # 11.0000000000000
+  Yb:      Yb          # 24.0000000000000
+ #Yb:      Yb_2        #  8.00000000000000
+ #Zn:      Zn          # 12.0000000000000
+ #Zn:      Zn_GW       # 12.0000000000000
+ #Zn:      Zn_pv_GW    # 18.0000000000000
+  Zn:      Zn_sv_GW    # 20.0000000000000
+  Zr:      Zr_sv       # 12.0000000000000
+ #Zr:      Zr_sv_GW    # 12.0000000000000
+

data/test/test_incar.rb

@@ -117,11 +117,51 @@ class TC_Incar < Test::Unit::TestCase
     assert_raise(Errno::ENOENT){VaspUtils::Incar.load_file("")}
   end
 
-  #def test_dump
-  # 
-  # 
-  # TODO
-  #end
+  def test_dump
+    pairs = {
+      "SYSTEM" => "dummy",
+      "PREC" => "High",
+      "ENCUT" => "400",
+      "EDIFF" => "1.0e-05",
+      "LREAL" => ".TRUE.",
+    }
+
+    assert_equal(
+      [
+        "SYSTEM = dummy",
+        "PREC = High",
+        "ENCUT = 400",
+        "EDIFF = 1.0e-05",
+        "LREAL = .TRUE.",
+      ].join("\n"),
+      VaspUtils::Incar.dump(pairs)
+    )
 
+    assert_equal(
+      [
+        "SYSTEM = dummy",
+        "PREC = High",
+        "ENCUT = 400",
+        "EDIFF = 1.0e-05",
+        "LREAL = .TRUE.",
+      ].join("\n"),
+      VaspUtils::Incar.dump(pairs, nil)
+    )
+
+    outfile = "test/incar/tmp.incar"
+    FileUtils.rm outfile if File.exist? outfile
+    File.open(outfile, "w") { |io| VaspUtils::Incar.dump(pairs, io) }
+    assert_equal(
+      [
+        "SYSTEM = dummy",
+        "PREC = High",
+        "ENCUT = 400",
+        "EDIFF = 1.0e-05",
+        "LREAL = .TRUE.",
+      ].join("\n"),
+      File.open(outfile).read
+    )
+    FileUtils.rm outfile if File.exist? outfile
+  end
 end
 

data/test/test_poscar.rb

@@ -46,7 +46,7 @@ class TC_Poscar < Test::Unit::TestCase
     cell = Cell.new(axes, atoms)
     cell.comment = "test"
     io = StringIO.new
-    VaspUtils::Poscar.dump(cell, [0,1], io)
+    VaspUtils::Poscar.dump(cell, [0,1], io, 4)
     io.rewind
     corrects = [
       "test\n",
@@ -66,6 +66,7 @@ class TC_Poscar < Test::Unit::TestCase
     end
     assert_equal(corrects.size, lines.size)
 
+    # vasp 4
     atoms = [
       Atom.new(0, [0.1, 0.2, 0.3], "atom0", [false, true , true ]),
       Atom.new(1, [0.2, 0.3, 0.4], "atom1", [false, false, true ]),
@@ -74,7 +75,7 @@ class TC_Poscar < Test::Unit::TestCase
     cell = Cell.new(axes, atoms)
     cell.comment = "test"
     io = StringIO.new
-    VaspUtils::Poscar.dump(cell, [0,1], io)
+    VaspUtils::Poscar.dump(cell, [0,1], io, 4)
     io.rewind
     corrects = [
       "test\n",
@@ -94,12 +95,73 @@ class TC_Poscar < Test::Unit::TestCase
       assert_equal(cor, lines[index], "line: #{index}")
     end
     assert_equal(corrects.size, lines.size)
+
+    atoms = [
+      Atom.new(0, [0.1, 0.2, 0.3], "atom0", [false, true , true ]),
+      Atom.new(1, [0.2, 0.3, 0.4], "atom1", [false, false, true ]),
+      Atom.new(0, [0.3, 0.4, 0.5], "atom2", [false, false, false]),
+    ]
+    cell = Cell.new(axes, atoms)
+    cell.comment = "test"
+    io = StringIO.new
+    VaspUtils::Poscar.dump(cell, [0,1], io, 4)
+    io.rewind
+    corrects = [
+      "test\n",
+      "1.0\n",
+      "   1.000000000000000   0.000000000000000   0.000000000000000\n",
+      "   0.000000000000000   1.000000000000000   0.000000000000000\n",
+      "   0.000000000000000   0.000000000000000   1.000000000000000\n",
+      "2 1\n",
+      "Selective dynamics\n",
+      "Direct\n",
+      "   0.100000000000000   0.200000000000000   0.300000000000000 F T T\n",
+      "   0.300000000000000   0.400000000000000   0.500000000000000 F F F\n",
+      "   0.200000000000000   0.300000000000000   0.400000000000000 F F T\n",
+    ]
+    lines = io.readlines
+    corrects.each_with_index do |cor, index|
+      assert_equal(cor, lines[index], "line: #{index}")
+    end
+    assert_equal(corrects.size, lines.size)
+    # vasp 5
+    atoms = [
+      Atom.new("Li", [0.1, 0.2, 0.3], "atom0", [false, true , true ]),
+      Atom.new("O" , [0.2, 0.3, 0.4], "atom1", [false, false, true ]),
+      Atom.new("Li", [0.3, 0.4, 0.5], "atom2", [false, false, false]),
+    ]
+    cell = Cell.new(axes, atoms)
+    cell.comment = "test"
+    io = StringIO.new
+    VaspUtils::Poscar.dump(cell, ["Li", "O"], io, 5)
+    io.rewind
+    corrects = [
+      "test\n",
+      "1.0\n",
+      "   1.000000000000000   0.000000000000000   0.000000000000000\n",
+      "   0.000000000000000   1.000000000000000   0.000000000000000\n",
+      "   0.000000000000000   0.000000000000000   1.000000000000000\n",
+      "Li O\n",
+      "2 1\n",
+      "Selective dynamics\n",
+      "Direct\n",
+      "   0.100000000000000   0.200000000000000   0.300000000000000 F T T\n",
+      "   0.300000000000000   0.400000000000000   0.500000000000000 F F F\n",
+      "   0.200000000000000   0.300000000000000   0.400000000000000 F F T\n",
+    ]
+    lines = io.readlines
+    corrects.each_with_index do |cor, index|
+      assert_equal(cor, lines[index], "line: #{index}")
+    end
+    assert_equal(corrects.size, lines.size)
+
   end
 
   def test_parse
     io = StringIO.new
     assert_raises(VaspUtils::Poscar::ParseError){ VaspUtils::Poscar.parse(io) }
 
+    # vasp 4 style
     io = StringIO.new
     io.puts "sample0"
     io.puts "1.0"
@@ -129,6 +191,7 @@ class TC_Poscar < Test::Unit::TestCase
     assert_equal(
       Atom.new(2, [0.5, 0.5, 0.0], "#O--003"), cell.atoms[2])
 
+    # vasp 4 style and selective dynamics
     io = StringIO.new
     io.puts "sample1"
     io.puts "2.0"
@@ -165,10 +228,41 @@ class TC_Poscar < Test::Unit::TestCase
     assert_equal(
       Atom.new(2, [0.5, 0.5, 0.5], "#O--004", [true, true, true]),
       cell.atoms[3])
+
+    # vasp 5 style
+    io = StringIO.new
+    io.puts "sample0"
+    io.puts "1.0"
+    io.puts "    1.0  0.0  0.0"
+    io.puts "    0.0  1.0  0.0"
+    io.puts "    0.0  0.0  1.0"
+    io.puts " Li Ge O"
+    io.puts " 1  1  1"
+    io.puts "Direct"
+    io.puts "    0.0  0.0  0.0  #Li-001"
+    io.puts "    0.5  0.0  0.0  #Ge-002"
+    io.puts "    0.5  0.5  0.0  #O--003"
+    io.rewind
+    cell = VaspUtils::Poscar.parse(io)
+    assert_equal("sample0", cell.comment)
+    assert_equal(
+      LatticeAxes.new( [
+        [1.0, 0.0, 0.0 ],
+        [0.0, 1.0, 0.0 ],
+        [0.0, 0.0, 1.0 ],
+      ]),
+      cell.axes
+    )
+    assert_equal(
+      Atom.new("Li", [0.0, 0.0, 0.0], "#Li-001"), cell.atoms[0])
+    assert_equal(
+      Atom.new("Ge", [0.5, 0.0, 0.0], "#Ge-002"), cell.atoms[1])
+    assert_equal(
+      Atom.new("O", [0.5, 0.5, 0.0], "#O--003"), cell.atoms[2])
   end
 
   def test_load_file
-    cell = VaspUtils::Poscar.load_file("test/poscar/POSCAR.00")
+    cell = VaspUtils::Poscar.load_file("test/poscar/POSCAR.4-0")
     assert_equal("sample0", cell.comment)
     assert_equal(
       LatticeAxes.new( [
@@ -185,26 +279,5 @@ class TC_Poscar < Test::Unit::TestCase
     assert_equal(
       Atom.new(2, [0.5, 0.5, 0.0], "#O--003"), cell.atoms[2])
 
-    #cell = VaspUtils::Poscar.load_file("test/poscar/POSCAR.02")
-    #assert_equal("sample0", cell.comment)
-    #assert_in_delta( 7.1028554188641708, cell.axes[0][0], $tolerance)
-    #assert_in_delta(-0.0000000169534433, cell.axes[0][1], $tolerance)
-    #assert_in_delta(-0.0000000169534428, cell.axes[0][2], $tolerance)
-    #assert_in_delta( 0.0000001136137521, cell.axes[1][0], $tolerance) 
-    #assert_in_delta( 7.1028554188641725, cell.axes[1][1], $tolerance) 
-    #assert_in_delta(-0.0000000169534433, cell.axes[1][2], $tolerance) 
-    #assert_in_delta( 0.0000001136137521, cell.axes[2][0], $tolerance) 
-    #assert_in_delta( 0.0000001136137521, cell.axes[2][1], $tolerance) 
-    #assert_in_delta( 7.1028554188641725, cell.axes[2][2], $tolerance) 
-    #assert_equal(0, cell.atoms[0].element)
-    #assert_equal(0.0395891220708791, cell.atoms[0].position[0]) 
-    #assert_equal(0.0395891220708791, cell.atoms[0].position[1])
-    #assert_equal(0.0395891220708791, cell.atoms[0].position[2])
-
   end
-
-  #def setup
-  # #@pp02 = VaspUtils::Poscar.new("test/poscar/POSCAR.shirai")
-  #end
-
 end

data/test/test_potcar.rb

@@ -3,6 +3,7 @@
 require "test/unit"
 require "vasputils.rb"
 require "vasputils/potcar.rb"
+require "vasputils/setting.rb"
 
 class TC_Potcar < Test::Unit::TestCase
 
@@ -40,27 +41,5 @@ class TC_Potcar < Test::Unit::TestCase
     assert_equal( correct, @p2[:elements])
   end
 
-  #def test_self_elements
-  # assert_equal([ "Li", "Ge", "O" ], VaspUtils::Potcar.elements( @p0 ))
-  # assert_equal([ "Li", "Ge", "O" ], VaspUtils::Potcar.elements( @p1 ))
-  # correct = [
-  #   "Ac", "Ac", "Ag", "Al", "Al", "Ar", "As", "Au", "B", "B", "B", "Ba",
-  #   "Be", "Be", "Bi", "Bi", "Br", "C", "C", "C", "Ca", "Ca", "Cd", "Ce",
-  #   "Ce", "Cl", "Cl", "Co", "Cr", "Cr", "Cs", "Cu", "Cu", "Dy",
-  #   "Er", "Er", "Eu", "Eu", "F", "F", "F", "Fe", "Fe", "Ga", "Ga", "Ga",
-  #   "Gd", "Gd", "Ge", "Ge", "Ge", "H", "H", "H", "H", "H", "H", "He",
-  #   "Hf", "Hf", "Hg", "Ho", "I", "In", "In", "Ir", "K", "K", "Kr",
-  #   "La", "La", "Li", "Li", "Lu", "Lu", "Mg", "Mg", "Mn", "Mn",
-  #   "Mo", "Mo", "N", "N", "N", "Na", "Na", "Na", "Nb", "Nb", "Nd", "Nd",
-  #   "Ne", "Ni", "Ni", "Np", "Np", "O", "O", "O", "Os", "Os", "P", "P",
-  #   "Pa", "Pa", "Pb", "Pb", "Pd", "Pd", "Pm", "Pm", "Pr", "Pr", "Pt",
-  #   "Pu", "Pu", "Rb", "Rb", "Re", "Re", "Rh", "Rh", "Ru", "Ru", "S", "S",
-  #   "Sb", "Sc", "Se", "Si", "Si", "Sm", "Sm", "Sn", "Sn", "Sr",
-  #   "Ta", "Ta", "Tb", "Tc", "Tc", "Te", "Th", "Th", "Ti", "Ti", "Ti",
-  #   "Tl", "Tl", "Tm", "Tm", "U", "U", "V", "V", "V", "W", "W", "X", "Y",
-  #   "Yb", "Yb", "Zn", "Zr", "Zr"]
-  # assert_equal( correct, VaspUtils::Potcar.elements( @p2 ))
-  #end
-
 end
 

data/test/test_potcar_concatenater.rb

@@ -0,0 +1,56 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "test/unit"
+require "vasputils.rb"
+#require "vasputils/setting.rb"
+#require "vasputils/potcar/concatenater.rb"
+
+class VaspUtils::Potcar::Concatenater
+  public :dump
+end
+
+class TC_Concatenater < Test::Unit::TestCase
+  def setup
+    settings = VaspUtils::Setting.new("test/potcar/test.vasputils")
+    potcar_path = settings["potcar_path"]
+    elem_potcar = settings["element_potcar"]
+
+    @c = VaspUtils::Potcar::Concatenater.new(potcar_path, elem_potcar)
+  end
+
+  def test_dump
+    # concatenating
+    assert_equal(
+      "H\n",
+      @c.dump(["H"])
+    )
+    assert_equal(
+      "H\nLi_sv\n",
+      @c.dump(["H", "Li"])
+    )
+    assert_raise(VaspUtils::Potcar::Concatenater::NoPotcarError){@c.dump(["H", "Li", "not_exist_element"])}
+
+
+    # return string if io is nil.
+    assert_equal(
+      "H\n",
+      @c.dump(["H"], nil)
+    )
+
+    # write io
+    outfile = "test/potcar/tmp.POTCAR"
+    FileUtils.rm(outfile) if File.exist? outfile
+    File.open(outfile, "w") do |io|
+      @c.dump(["H"], io)
+    end
+    assert_equal(
+      "H\n",
+      File.read(outfile)
+    )
+
+    FileUtils.rm(outfile) if File.exist? outfile
+  end
+
+end
+

data/test/test_setting.rb

@@ -0,0 +1,23 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "test/unit"
+require "vasputils/setting.rb"
+
+class TC_Setting < Test::Unit::TestCase
+  def setup
+    @s = VaspUtils::Setting.new("example/dot.vasputils")
+  end
+
+  def test_initialize
+    assert_raise(Errno::ENOENT){VaspUtils::Setting.new("not_exist_file")}
+  end
+
+  def test_get
+    #assert_raise(VaspUtils::Setting::NoEntryError){@s.get("no_entory_key")}
+    #assert_equal("/usr/local/calc/potcar/potpaw_PBE.52", @s.get("potcar_dir"))
+    assert_raise(VaspUtils::Setting::NoEntryError){@s["no_entory_key"]}
+    assert_equal("/usr/local/calc/potcar/potpaw_PBE.52", @s["potcar_dir"])
+  end
+end
+