Added many test files

scripts/qp_plugins

@@ -39,7 +39,7 @@ try:
     from docopt import docopt
     from module_handler import ModuleHandler, get_dict_child
     from module_handler import get_l_module_descendant
-    from qp_path import QP_SRC, QP_PLUGINS, QP_ROOT
+    from qp_path import QP_SRC, QP_PLUGINS, QP_ROOT, QP_DATA
 except ImportError:
     print "Please check if you have sourced the ${QP_ROOT}/quantum_package.rc"
     print "(`source ${QP_ROOT}/quantum_package.rc`)"
@@ -73,6 +73,11 @@ def save_new_module(path, l_child):
     with open(os.path.join(path, "README.rst"), "w") as f:
         f.write(header + "\n")
 
+    with open(os.path.join(path, ".gitignore"), "w") as f:
+        with open(os.path.join(QP_DATA, "module_gitignore"), "r") as g:
+            data = g.read()
+        f.write(data)
+
     with open(os.path.join(path, "%s.irp.f"%(module_name) ), "w") as f:
         f.write("program {0}".format(module_name) )
         f.write("""

scripts/utility/qp_path.py

@@ -10,8 +10,9 @@ except:
     print "source quantum_package.rc"
     sys.exit(1)
 else:
-    QP_SRC = os.path.join(QP_ROOT, "src")
+    QP_EZFIO   = os.environ["QP_EZFIO"]
+    QP_SRC     = os.path.join(QP_ROOT, "src")
     QP_PLUGINS = os.path.join(QP_ROOT, "plugins")
-    QP_EZFIO = os.environ["QP_EZFIO"]
-    QP_OCAML = os.path.join(QP_ROOT, "ocaml")
-    QP_TESTS = os.path.join(QP_ROOT, "tests")
+    QP_OCAML   = os.path.join(QP_ROOT, "ocaml")
+    QP_TESTS   = os.path.join(QP_ROOT, "tests")
+    QP_DATA    = os.path.join(QP_ROOT, "data")

src/ezfio_files/00.create.bats

@@ -0,0 +1,108 @@
+#!/usr/bin/env bats
+
+source $QP_ROOT/tests/bats/common.bats.sh
+
+function run {
+  INPUT=$1
+  EZ=${INPUT/.xyz/.ezfio}
+  MULT=$2
+  CHARGE=$3
+  BASIS=$4
+  if [[ -n $5 ]] ; then 
+    PSEUDO="-p $5"
+  fi
+  cp ${QP_ROOT}/tests/input/$INPUT .
+  rm -rf $EZ
+  qp_create_ezfio_from_xyz $INPUT -b "$BASIS" -m $MULT -c $CHARGE $PSEUDO -o $EZ
+  qp_edit -c $EZ
+}
+
+
+@test "qp_create c2h2.xyz" {
+  run c2h2.xyz 1 0 vdz-bfd bfd
+}
+
+@test "qp_create clo.xyz" {
+  run clo.xyz 2 0 cc-pvdz
+}
+
+@test "qp_create dhno.xyz" {
+  run dhno.xyz 2 0 chipman-dzp
+}
+
+@test "qp_create h3coh.xyz" {
+  run h3coh.xyz 1 0 6-31g
+}
+
+@test "qp_create hcn.xyz" {
+  run hcn.xyz 1 0 aug-cc-pvdz
+}
+
+@test "qp_create n2.xyz" {
+  run n2.xyz 1 0 cc-pvtz
+}
+
+@test "qp_create sih2_3b1.xyz" {
+  run sih2_3b1.xyz 1 0 6-31g
+}
+
+@test "qp_create so.xyz" {
+  run so.xyz 3 0 vdz-bfd bfd
+}
+
+@test "qp_create ch4.xyz" {
+  run ch4.xyz 1 0 aug-cc-pvtz
+}
+
+@test "qp_create co2.xyz" {
+  run co2.xyz 1 0 cc-pvdz
+}
+
+@test "qp_create f2.xyz" {
+  run f2.xyz 1 0 "Def2-TZVP"
+}
+
+@test "qp_create h2o.xyz" {
+  run h2o.xyz 1 0 cc-pvdz
+}
+
+@test "qp_create hco.xyz" {
+  run hco.xyz 2 0 "Ahlrichs VDZ"
+}
+
+@test "qp_create nh3.xyz" {
+  run nh3.xyz 1 0 cc-pvdz
+}
+
+@test "qp_create sih3.xyz" {
+  run sih3.xyz 2 0 vdz-bfd bfd
+}
+
+@test "qp_create clf.xyz" {
+  run clf.xyz 1 0 cc-pvdz
+}
+
+@test "qp_create h2o2.xyz" {
+  run h2o2.xyz 1 0 cc-pvdz
+}
+
+@test "qp_create h2s.xyz" {
+  run h2s.xyz 1 0 cc-pvdz
+}
+
+@test "qp_create hbo.xyz" {
+  run hbo.xyz 1 0 cc-pvtz
+}
+
+@test "qp_create n2h4.xyz" {
+  run n2h4.xyz 1 0 cc-pvdz
+}
+
+@test "qp_create oh.xyz" {
+  run oh.xyz 2 0 "Roos Augmented Double Zeta ANO"
+}
+
+@test "qp_create so2.xyz" {
+  run so2.xyz 1 0 vtz-bfd bfd
+}
+

src/ezfio_files/01.convert.bats

@@ -0,0 +1,24 @@
+#!/usr/bin/env bats
+
+source $QP_ROOT/tests/bats/common.bats.sh
+
+function run {
+  INPUT=$1
+  EZ=${INPUT}.ezfio
+  cp ${QP_ROOT}/tests/input/$INPUT .
+  qp_convert_output_to_ezfio $INPUT
+  qp_edit -c $EZ
+}
+
+#=== Convert
+@test "gamess convert hbo.gms.out" {
+  run hbo.gms.out 
+}
+
+@test "g09 convert h2o.log" {
+  run h2o.log 
+}
+
+@test "gamess convert cu_nh3_4_2plus.gms.out" {
+  run cu_nh3_4_2plus.gms.out 
+}

src/ezfio_files/10.convert.bats

@@ -1,27 +0,0 @@
-#!/usr/bin/env bats
-
-source $QP_ROOT/tests/bats/common.bats.sh
-
-#=== Convert
-@test "gamess convert HBO.out" {
-  cp ${QP_ROOT}/tests/input/HBO.out .
-  qp_convert_output_to_ezfio HBO.out
-  qp_edit -c HBO.out.ezfio 
-  ezfio set_file HBO.out.ezfio
-  qp_run scf HBO.out.ezfio 
-  # Check energy
-  energy="$(ezfio get hartree_fock energy)"
-  eq $energy -100.0185822590964 1.e-10
-}
-
-@test "g09 convert H2O.log" {
-  cp ${QP_ROOT}/tests/input/h2o.log .
-  qp_convert_output_to_ezfio h2o.log
-  qp_edit -c h2o.log.ezfio 
-  ezfio set_file h2o.log.ezfio
-  qp_run scf h2o.log.ezfio 
-  # Check energy
-  energy="$(ezfio get hartree_fock energy)"
-  eq $energy -76.0270218704265 1E-10
-}
-

tests/input/c2h2.xyz

@@ -0,0 +1,6 @@
+4
+C2H2 Geo: Experiment Mult: 1 symmetry: 14
+C    0.0    0.0    0.6013
+C    0.0    0.0    -0.6013
+H    0.0    0.0    1.6644
+H    0.0    0.0    -1.6644

tests/input/ch4.xyz

@@ -0,0 +1,7 @@
+5
+CH4 Geo: Experiment Mult: 1 symmetry: 10
+C    0.0    0.0    0.0
+H    0.6276    0.6276    0.6276
+H    0.6276    -0.6276    -0.6276
+H    -0.6276    0.6276    -0.6276
+H    -0.6276    -0.6276    0.6276

tests/input/clf.xyz

@@ -0,0 +1,4 @@
+2
+ClF Geo: Experiment Mult: 1 symmetry: 26
+Cl    0.0    0.0    1.6283
+F    0.0    0.0    0.0

tests/input/clo.xyz

@@ -0,0 +1,4 @@
+2
+ClO Geo: Experiment Mult: 2 symmetry: 25
+Cl    0.0    0.0    1.5696
+O    0.0    0.0    0.0

tests/input/co2.xyz

@@ -0,0 +1,5 @@
+3
+CO2 Geo: Experiment Mult: 1 symmetry: 22
+C    0.0    0.0    0.0
+O    0.0    0.0    1.1621
+O    0.0    0.0    -1.1621

tests/input/f2.xyz

@@ -0,0 +1,4 @@
+2
+F2 Geo: Experiment Mult: 1 symmetry: 18
+F    0.0    0.0    0.0
+F    0.0    0.0    1.4119

tests/input/h2o2.xyz

@@ -0,0 +1,6 @@
+4
+H2O2 Geo: Experiment Mult: 1 symmetry: 18
+H    0.819    0.817    0.422
+H    -0.819    -0.817    0.422
+O    0.0    0.7375    -0.0528
+O    0.0    -0.7375    -0.0528

tests/input/h2s.xyz

@@ -0,0 +1,5 @@
+3
+H2S Geo: Experiment Mult: 1 symmetry: 18
+H    0.0    0.9569    0.9208
+H    0.0    -0.9569    0.9208
+S    0.0    0.0    0.0

tests/input/h3coh.xyz

@@ -0,0 +1,8 @@
+6
+H3COH Geo: Experiment Mult: 1 symmetry: 18
+C    -0.0503    0.6685    0.0
+H    -1.0807    1.0417    0.0
+H    0.465    1.0417    0.8924
+H    0.465    1.0417    -0.8924
+H    0.8544    -1.0677    0.0
+O    -0.0503    -0.7585    0.0

tests/input/hcn.xyz

@@ -0,0 +1,5 @@
+3
+HCN Geo: Experiment Mult: 1 symmetry: 14
+C    0.0    0.0    0.0
+H    0.0    0.0    1.064
+N    0.0    0.0    -1.156

tests/input/hco.xyz

@@ -0,0 +1,5 @@
+3
+HCO Geo: Experiment Mult: 2 symmetry: 15
+C    0.0    0.0    0.0
+H    1.08    0.0    0.0
+O    -0.5899    1.0427    0.0

tests/input/n2.xyz

@@ -0,0 +1,4 @@
+2
+N2 Geo: Experiment Mult: 1 symmetry: 14
+N    0.0    0.0    0.5488
+N    0.0    0.0    -0.5488

tests/input/n2h4.xyz

@@ -0,0 +1,8 @@
+6
+N2H4 Geo: Experiment Mult: 1 symmetry: 18
+H    -0.447    1.0031    0.7562
+H    0.447    -1.0031    0.7562
+H    0.9663    1.0031    0.0301
+H    -0.9663    -1.0031    0.0301
+N    0.0    0.723    -0.1123
+N    0.0    -0.723    -0.1123

tests/input/nh3.xyz

@@ -0,0 +1,6 @@
+4
+NH3 Geo: Experiment Mult: 1 symmetry: 10
+H    0.0    -0.9377    -0.3816
+H    0.8121    0.4689    -0.3816
+H    -0.8121    0.4689    -0.3816
+N    0.0    0.0    0.0

tests/input/oh.xyz

@@ -0,0 +1,4 @@
+2
+OH Geo: Experiment Mult: 2 symmetry: 9
+H    0.0    0.0    0.9697
+O    0.0    0.0    0.0

tests/input/sih2_3b1.xyz

@@ -0,0 +1,5 @@
+3
+SiH2_3B1 Geo: Experiment Mult: 3 symmetry: 16
+H    0.0    1.273174    -0.665412
+H    0.0    -1.273174    -0.665412
+Si    0.0    0.0    0.095059

tests/input/sih3.xyz

@@ -0,0 +1,6 @@
+4
+SiH3 Geo: Experiment Mult: 2 symmetry: 17
+H    0.0    1.3928    -0.382
+H    1.2062    -0.6964    -0.382
+H    -1.2062    -0.6964    -0.382
+Si    0.0    0.0    0.0819

tests/input/so.xyz

@@ -0,0 +1,4 @@
+2
+SO Geo: Experiment Mult: 3 symmetry: 24
+O    0.0    0.0    1.4811
+S    0.0    0.0    0.0

tests/input/so2.xyz

@@ -0,0 +1,5 @@
+3
+SO2 Geo: Experiment Mult: 1 symmetry: 32
+O    0.0    1.2371    0.7215
+O    0.0    -1.2371    0.7215
+S    0.0    0.0    0.0