Merge branch 'dev' of github.com:QuantumPackage/qp2 into dev

bin/qp_test

@@ -60,19 +60,14 @@ def main(arguments):
         print("Running tests for %s"%(bats_file))
         print("")
         if arguments["-v"]:
-            p = None
             if arguments["TEST"]:
                 test = "export TEST=%s ; "%arguments["TEST"]
             else:
                 test = ""
-            try:
+            os.system(test+" python3 bats_to_sh.py "+bats_file+
-                os.system(test+" python3 bats_to_sh.py "+bats_file+
                                     "| bash")
-            except:
-                if p:
-                    p.terminate()
         else:
-            subprocess.check_call(["bats", bats_file], env=os.environ)
+            subprocess.check_call(["bats", "--verbose-run", "--trace", bats_file], env=os.environ)
 
 
 

configure

@@ -281,8 +281,8 @@ EOF
 
             execute << EOF
               cd "\${QP_ROOT}"/external
-              tar -zxf qp2-dependencies/bats-v1.1.0.tar.gz
+              tar -zxf qp2-dependencies/bats-v1.7.0.tar.gz
-              ( cd bats-core-1.1.0/ ; ./install.sh \${QP_ROOT})
+              ( cd bats-core-1.7.0/ ; ./install.sh \${QP_ROOT})
 EOF
 
     else

external/qp2-dependencies

@@ -1 +1 @@
-Subproject commit 90ee61f5041c7c94a0c605625a264860292813a0
+Subproject commit 242151e03d1d6bf042387226431d82d35845686a

ocaml/Qputils.ml

@@ -56,3 +56,7 @@ let string_of_string s = s
 let list_map f l =
   List.rev_map f l
   |> List.rev
+
+let socket_convert socket =
+    ((Obj.magic (Obj.repr socket)) : [ `Xsub ] Zmq.Socket.t )
+

ocaml/qp_tunnel.ml

@@ -2,7 +2,7 @@ open Qputils
 open Qptypes
 
 type ezfio_or_address = EZFIO of string | ADDRESS of string
-type req_or_sub = REQ | SUB 
+type req_or_sub = REQ | SUB
 
 let localport = 42379
 
@@ -29,7 +29,7 @@ let () =
   end;
 
   let arg =
-    let x = 
+    let x =
       match Command_line.anon_args () with
       | [x] -> x
       | _ -> begin
@@ -44,7 +44,7 @@ let () =
   in
 
 
-  let localhost = 
+  let localhost =
      Lazy.force TaskServer.ip_address
   in
 
@@ -52,28 +52,28 @@ let () =
   let long_address  =
     match arg with
     | ADDRESS x -> x
-    | EZFIO   x -> 
+    | EZFIO   x ->
-	let ic = 
+	let ic =
 	  Filename.concat  (Qpackage.ezfio_work x)  "qp_run_address"
           |> open_in
 	in
-        let result = 
+        let result =
           input_line ic
           |> String.trim
         in
         close_in ic;
         result
   in
-  
+
   let protocol, address, port =
     match String.split_on_char ':' long_address with
     | t :: a :: p :: [] -> t, a, int_of_string p
-    | _ -> failwith @@ 
+    | _ -> failwith @@
            Printf.sprintf "%s : Malformed address" long_address
   in
 
 
-  let zmq_context = 
+  let zmq_context =
     Zmq.Context.create ()
   in
 
@@ -105,10 +105,10 @@ let () =
 
 
   let create_socket  sock_type  bind_or_connect  addr =
-    let socket = 
+    let socket =
       Zmq.Socket.create zmq_context sock_type
     in
-    let () = 
+    let () =
       try
         bind_or_connect socket addr
       with
@@ -131,37 +131,64 @@ let () =
   Sys.set_signal  Sys.sigint   handler;
 
 
-  let new_thread req_or_sub addr_in addr_out =
+  let new_thread_req addr_in addr_out =
     let socket_in, socket_out =
-      match req_or_sub with
-      | REQ ->
           create_socket  Zmq.Socket.router  Zmq.Socket.bind     addr_in,
           create_socket  Zmq.Socket.dealer  Zmq.Socket.connect  addr_out
-      | SUB ->
-          create_socket  Zmq.Socket.sub  Zmq.Socket.connect  addr_in,
-          create_socket  Zmq.Socket.pub  Zmq.Socket.bind     addr_out
     in
 
-    if req_or_sub = SUB then
-        Zmq.Socket.subscribe  socket_in  "";
 
-
+    let action_in =
-
+        fun () -> Zmq.Socket.recv_all  socket_in  |> Zmq.Socket.send_all  socket_out
-   let action_in = 
-      match req_or_sub with
-        | REQ -> (fun () -> Zmq.Socket.recv_all  socket_in  |> Zmq.Socket.send_all  socket_out)
-        | SUB -> (fun () -> Zmq.Socket.recv_all  socket_in  |> Zmq.Socket.send_all  socket_out)
     in
 
-    let action_out = 
+    let action_out =
-      match req_or_sub with
+        fun () -> Zmq.Socket.recv_all  socket_out |> Zmq.Socket.send_all  socket_in
-        | REQ -> (fun () -> Zmq.Socket.recv_all  socket_out |> Zmq.Socket.send_all  socket_in )
-        | SUB -> (fun () -> () )
     in
 
     let pollitem =
       Zmq.Poll.mask_of
-        [| (socket_in,  Zmq.Poll.In) ; (socket_out, Zmq.Poll.In) |]
+        [| (socket_convert socket_in,  Zmq.Poll.In) ; (socket_convert socket_out, Zmq.Poll.In) |]
+    in
+
+    while !run_status do
+
+        let polling =
+          Zmq.Poll.poll  ~timeout:1000  pollitem
+        in
+
+        match polling with
+          | [| Some Zmq.Poll.In ; Some Zmq.Poll.In |]     -> ( action_out () ; action_in () )
+          | [| _                ; Some Zmq.Poll.In |]     ->   action_out ()
+          | [| Some Zmq.Poll.In ; _                |]     ->   action_in  ()
+          | _                    -> ()
+    done;
+
+    Zmq.Socket.close  socket_in;
+    Zmq.Socket.close  socket_out;
+  in
+
+  let new_thread_sub addr_in addr_out =
+    let socket_in, socket_out =
+          create_socket  Zmq.Socket.sub  Zmq.Socket.connect  addr_in,
+          create_socket  Zmq.Socket.pub  Zmq.Socket.bind     addr_out
+    in
+
+    Zmq.Socket.subscribe  socket_in  "";
+
+
+
+   let action_in =
+        fun () -> Zmq.Socket.recv_all  socket_in  |> Zmq.Socket.send_all  socket_out
+    in
+
+    let action_out =
+        fun () -> ()
+    in
+
+    let pollitem =
+      Zmq.Poll.mask_of
+        [| (socket_convert socket_in,  Zmq.Poll.In) ; (socket_convert socket_out, Zmq.Poll.In) |]
     in
 
 
@@ -173,8 +200,8 @@ let () =
 
         match polling with
           | [| Some Zmq.Poll.In ; Some Zmq.Poll.In |]     -> ( action_out () ; action_in () )
-          | [| _                ; Some Zmq.Poll.In |]     ->   action_out () 
+          | [| _                ; Some Zmq.Poll.In |]     ->   action_out ()
-          | [| Some Zmq.Poll.In ; _                |]     ->   action_in  () 
+          | [| Some Zmq.Poll.In ; _                |]     ->   action_in  ()
           | _                    -> ()
     done;
 
@@ -193,8 +220,8 @@ let () =
       Printf.sprintf "tcp://*:%d"  localport
     in
 
-    let f () = 
+    let f () =
-      new_thread  REQ  addr_in  addr_out
+      new_thread_req  addr_in  addr_out
     in
 
     (Thread.create f) ()
@@ -211,8 +238,8 @@ let () =
       Printf.sprintf "tcp://*:%d" (localport+2)
     in
 
-    let f () = 
+    let f () =
-      new_thread  REQ  addr_in  addr_out
+      new_thread_req  addr_in  addr_out
     in
     (Thread.create f) ()
   in
@@ -227,8 +254,8 @@ let () =
       Printf.sprintf "tcp://*:%d" (localport+1)
     in
 
-    let f () = 
+    let f () =
-      new_thread  SUB  addr_in  addr_out
+      new_thread_sub  addr_in  addr_out
     in
     (Thread.create f) ()
   in
@@ -236,7 +263,7 @@ let () =
 
 
   let input_thread =
-    let f () = 
+    let f () =
       let addr_out =
         match arg with
         | EZFIO _ -> None
@@ -248,22 +275,22 @@ let () =
         Printf.sprintf "tcp://*:%d"  (localport+9)
       in
 
-      let socket_in = 
+      let socket_in =
         create_socket  Zmq.Socket.rep  Zmq.Socket.bind     addr_in
       in
 
       let socket_out =
-        match addr_out with 
+        match addr_out with
         | Some addr_out -> Some (
             create_socket  Zmq.Socket.req  Zmq.Socket.connect  addr_out)
         | None -> None
       in
 
-      let temp_file = 
+      let temp_file =
         Filename.temp_file "qp_tunnel" ".tar.gz"
       in
 
-      let get_ezfio_filename () = 
+      let get_ezfio_filename () =
         match arg with
         | EZFIO x -> x
         | ADDRESS _ ->
@@ -277,9 +304,9 @@ let () =
           end
       in
 
-      let get_input () = 
+      let get_input () =
         match arg with
-        | EZFIO x -> 
+        | EZFIO x ->
           begin
             Printf.sprintf "tar --exclude=\"*.gz.*\" -zcf %s %s" temp_file x
             |> Sys.command |> ignore;
@@ -291,11 +318,11 @@ let () =
             in
             ignore @@ Unix.lseek  fd  0  Unix.SEEK_SET ;
             let bstr =
-                Unix.map_file  fd  Bigarray.char 
+                Unix.map_file  fd  Bigarray.char
                   Bigarray.c_layout false [| len |]
                 |> Bigarray.array1_of_genarray
             in
-            let result = 
+            let result =
               String.init len (fun i -> bstr.{i}) ;
             in
             Unix.close fd;
@@ -313,7 +340,7 @@ let () =
           end
       in
 
-      let () = 
+      let () =
         match socket_out with
         | None -> ()
         | Some socket_out ->
@@ -329,7 +356,7 @@ let () =
           | ADDRESS _ ->
             begin
               Printf.printf "Getting input... %!";
-              let ezfio_filename = 
+              let ezfio_filename =
                 get_ezfio_filename ()
               in
               Printf.printf "%s%!" ezfio_filename;
@@ -343,7 +370,7 @@ let () =
               |> Sys.command |> ignore ;
               let oc =
                 Filename.concat  (Qpackage.ezfio_work ezfio_filename)  "qp_run_address"
-                |> open_out 
+                |> open_out
               in
               Printf.fprintf oc "tcp://%s:%d\n"  localhost  localport;
               close_out oc;
@@ -359,9 +386,9 @@ let () =
       let action () =
         match Zmq.Socket.recv socket_in with
         | "get_input" -> get_input ()
-                        |> Zmq.Socket.send socket_in 
+                        |> Zmq.Socket.send socket_in
         | "get_ezfio_filename" -> get_ezfio_filename ()
-                        |> Zmq.Socket.send socket_in 
+                        |> Zmq.Socket.send socket_in
         | "test" -> Zmq.Socket.send socket_in "OK"
         | x -> Printf.sprintf "Message '%s' not understood" x
                |> Zmq.Socket.send socket_in
@@ -372,7 +399,7 @@ On remote hosts, create ssh tunnel using:
  ssh -L %d:%s:%d -L %d:%s:%d -L %d:%s:%d -L %d:%s:%d %s &
 Or from this host connect to clients using:
  ssh -R %d:localhost:%d -R %d:localhost:%d -R %d:localhost:%d -R %d:localhost:%d <host> &
-%!" 
+%!"
                 (port  ) localhost (localport  )
                 (port+1) localhost (localport+1)
                 (port+2) localhost (localport+2)
@@ -392,12 +419,12 @@ Or from this host connect to clients using:
           match polling.(0) with
             | Some Zmq.Poll.In     -> action ()
             | None                 -> ()
-            | Some Zmq.Poll.In_out 
+            | Some Zmq.Poll.In_out
             | Some Zmq.Poll.Out    -> ()
 
       done;
 
-      let () = 
+      let () =
         match socket_out with
         | Some socket_out -> Zmq.Socket.close  socket_out
         | None -> ()
@@ -415,7 +442,7 @@ Or from this host connect to clients using:
   Thread.join ocaml_thread;
   Zmq.Context.terminate zmq_context;
   Printf.printf "qp_tunnel exited properly.\n"
-  
+
 
 
 

src/fci/40.fci.bats

@@ -37,48 +37,48 @@ function run_stoch() {
   qp set_file b2_stretched.ezfio
   qp set determinants n_det_max 10000
   qp set_frozen_core
-  run_stoch -49.14104086  0.0001  10000
+  run_stoch -49.14097596  0.0001  10000
 }
 
 @test "NH3" { # 0:00:11
   qp set_file nh3.ezfio
   qp set_mo_class --core="[1-4]" --act="[5-72]"
-  run -56.24474790 1.e-5  10000
+  run -56.24474908 1.e-5  10000
 }
 
 @test "DHNO" { # 0:00:10 
   qp set_file dhno.ezfio
   qp set_mo_class --core="[1-7]" --act="[8-64]"
-  run -130.45901042  1.e-4  10000
+  run -130.45904647  1.e-4  10000
 }
 
 @test "HCO" { # 0:01:16 
   qp set_file hco.ezfio
-  run_stoch -113.41658256  1.e-3  50000
+  run_stoch -113.41448940  2.e-3  50000
 }
 
 @test "H2O2" { # 0:01:48 
   qp set_file h2o2.ezfio
   qp set_mo_class --core="[1-2]" --act="[3-24]" --del="[25-38]"
-  run_stoch -151.02317880 2.e-3  100000
+  run_stoch -151.02437936 2.e-3  100000
 }
 
 @test "HBO" { # 0:00:46 
   [[ -n $TRAVIS ]] && skip
   qp set_file hbo.ezfio
-  run_stoch -100.22361288 1.e-4  50000
+  run_stoch -100.221198108988 2.e-3  50000
 }
 
 @test "H2O" { # 0:01:05 
   [[ -n $TRAVIS ]] && skip
   qp set_file h2o.ezfio
-  run_stoch -76.24347962  1.e-4  100000
+  run_stoch -76.241332121813  1.e-3  100000
 }
 
 @test "ClO" { # 0:03:07 
   [[ -n $TRAVIS ]] && skip
   qp set_file clo.ezfio
-  run_stoch -534.58202840  1.e-3  100000
+  run_stoch -534.573564655419 1.e-3  100000
 }
 
 @test "SO" { # 0:01:49 
@@ -90,99 +90,99 @@ function run_stoch() {
 @test "H2S" { # 0:01:12
   [[ -n $TRAVIS ]] && skip
   qp set_file h2s.ezfio
-  run_stoch -398.87187312  1.e-3  50000
+  run_stoch -398.865173546866 1.e-3  50000
 }
 
 @test "OH" { # 0:00:41
   [[ -n $TRAVIS ]] && skip
   qp set_file oh.ezfio
-  run_stoch -75.62393829  1.e-3  50000
+  run_stoch -75.6193013819546 1.e-3  50000
 }
 
 @test "SiH2_3B1" { # 0:00:50
   [[ -n $TRAVIS ]] && skip
   qp set_file sih2_3b1.ezfio
-  run_stoch -290.02083172  3.e-5  50000
+  run_stoch -290.01754869  3.e-5  50000
 }
 
 @test "H3COH" { # 0:01:05
   [[ -n $TRAVIS ]] && skip
   qp set_file h3coh.ezfio
-  run_stoch -115.22625460 2.e-3  50000
+  run_stoch -115.224147057725 2.e-3  50000
 }
 
 @test "SiH3" { # 0:01:09
   [[ -n $TRAVIS ]] && skip
   qp set_file sih3.ezfio
-  run_stoch -5.57818759  1.e-3  50000
+  run_stoch -5.57812512359276 1.e-3  50000
 }
 
 @test "CH4" { # 0:02:06
   [[ -n $TRAVIS ]] && skip
   qp set_file ch4.ezfio
   qp set_mo_class --core="[1]" --act="[2-30]" --del="[31-59]"
-  run_stoch -40.24195947  1.e-4  100000
+  run_stoch -40.2419474611994 1.e-4  100000
 }
 
 @test "ClF" { # 0:01:55 
   [[ -n $TRAVIS ]] && skip
   qp set_file clf.ezfio
-  run_stoch -559.20157348 1.e-3  50000
+  run_stoch -559.20666465 1.e-2  50000
 }
 
 @test "SO2" { # 0:00:24
   [[ -n $TRAVIS ]] && skip
   qp set_file so2.ezfio
   qp set_mo_class --core="[1-8]" --act="[9-87]"
-  run_stoch -41.57468087 1.e-4  50000
+  run_stoch -41.57468756 1.e-4  50000
 }
 
 @test "C2H2" { # 0:00:57 
   [[ -n $TRAVIS ]] && skip
   qp set_file c2h2.ezfio
   qp set_mo_class --act="[1-30]" --del="[31-36]"
-  run_stoch -12.38655876 1.e-3  50000
+  run_stoch -12.3862664765532 1.e-3  50000
 }
 
 @test "N2" { # 0:01:15
   [[ -n $TRAVIS ]] && skip
   qp set_file n2.ezfio
   qp set_mo_class --core="[1,2]" --act="[3-40]" --del="[41-60]"
-  run_stoch -109.31133266  2.e-3  50000
+  run_stoch -109.311954243348 2.e-3  50000
 }
 
 @test "N2H4" { # 0:00:51
   [[ -n $TRAVIS ]] && skip
   qp set_file n2h4.ezfio
   qp set_mo_class --core="[1-2]" --act="[3-24]" --del="[25-48]"
-  run_stoch -111.38161063  1.e-3 50000
+  run_stoch -111.38119165053 1.e-3 50000
 }
 
 @test "CO2" { # 0:01:00
   [[ -n $TRAVIS ]] && skip
   qp set_file co2.ezfio
   qp set_mo_class --core="[1,2]" --act="[3-30]" --del="[31-42]"
-  run_stoch -188.00154729  2.e-3  50000
+  run_stoch -188.002190327443 2.e-3  50000
 }
 
 @test "[Cu(NH3)4]2+" { # 0:01:53
   [[ -n $TRAVIS ]] && skip
   qp set_file cu_nh3_4_2plus.ezfio
   qp set_mo_class --core="[1-24]" --act="[25-45]" --del="[46-87]"
-  run_stoch -1862.98705091  1.e-05  50000
+  run_stoch -1862.98705340328 1.e-05  50000
 }
 
 @test "HCN" { # 0:01:26
   [[ -n $TRAVIS ]] && skip
   qp set_file hcn.ezfio
   qp set_mo_class --core="[1,2]" --act="[3-40]" --del="[41-55]"
-  run_stoch -93.09855896  5.e-4  50000
+  run_stoch -93.0980746734051 5.e-4  50000
 }
 
 @test "F2" { # 0:03:34
   [[ -n $TRAVIS ]] && skip
   qp set_file f2.ezfio
   qp set_frozen_core
-  run_stoch -199.30821487  0.002  100000
+  run_stoch -199.307512211742 0.002  100000
 }
 

src/iterations/print_extrapolation.irp.f

@@ -41,7 +41,7 @@ subroutine print_extrapolated_energy
   enddo
 
   print *,  ''
-  call ezfio_set_fci_energy_extrapolated(extrapolated_energy(2,1:N_states))
+  call ezfio_set_fci_energy_extrapolated(extrapolated_energy(min(N_iter,3),1:N_states))
 
 end subroutine
 

tests/bats/common.bats.sh

@@ -46,7 +46,7 @@ function test_exe() {
 
 run_only_test() {
   if [[ "$BATS_TEST_DESCRIPTION" != "$1" ]] && [[ "$BATS_TEST_NUMBER" != "$1" ]]; then
-    if [[ -z $BATS_TEST_FILENAME ]] ; then
+    if [[ -z "$BATS_TEST_FILENAME" ]] ; then
       exit 0
     else
       skip