Fixing small bugs

build.ninja

@@ -28,7 +28,7 @@ rule compile_ocaml_dep
   pool = console
 
 rule compile_ocaml
-  command = cd ocaml ; ninja $target
+  command = cd ocaml ; make $target
   description = Compiling OCaml tools
   pool = console
 

ezfio_config/qmc.config

@@ -8,12 +8,12 @@ ao_basis
   ao_expo            real          (ao_basis_ao_num,ao_basis_ao_prim_num_max)
 
 mo_basis
-  mo_tot_num         integer
-  mo_coef            real              (ao_basis_ao_num,mo_basis_mo_tot_num)
-  mo_classif         character         (mo_basis_mo_tot_num)
-  mo_energy          real              (mo_basis_mo_tot_num)
-  mo_occ             real              (mo_basis_mo_tot_num)
-  mo_symmetry        character*(8)     (mo_basis_mo_tot_num)
+  mo_num             integer
+  mo_coef            real              (ao_basis_ao_num,mo_basis_mo_num)
+  mo_classif         character         (mo_basis_mo_num)
+  mo_energy          real              (mo_basis_mo_num)
+  mo_occ             real              (mo_basis_mo_num)
+  mo_symmetry        character*(8)     (mo_basis_mo_num)
 
 electrons
   elec_alpha_num      integer

ocaml/Block.ml

@@ -86,7 +86,7 @@ let update_raw_data ?(locked=true) () =
   in
   let files = 
      let result = 
-       if Sys.is_directory dir_name then
+       if Sys.file_exists dir_name && Sys.is_directory dir_name then
          begin
            Sys.readdir dir_name
            |> Array.map (fun x -> dir_name^x)
@@ -150,7 +150,7 @@ let raw_data ?(locked=true) () =
 let properties = lazy (
   let h = Hashtbl.create 63 in
   List.iter (fun x -> 
-    Hashtbl.add h (Property.to_string x.property) x.property)
+    Hashtbl.replace h (Property.to_string x.property) x.property)
     (raw_data ());
   Hashtbl.fold (fun k v a -> v :: a) h []
 )

ocaml/Command_line.ml

@@ -166,7 +166,7 @@ let help () =
 
 
 
-let set_specs specs_in =
+let set_specs ?(no_help=false) specs_in =
     specs := { short='h' ;
                long ="help" ;
                doc  ="Prints the help message." ;
@@ -188,11 +188,20 @@ let set_specs specs_in =
                   )
     in
 
-    Getopt.parse_cmdline cmd_specs (fun x -> anon_args := !anon_args @ [x]);
+    let cmdline =
+      Sys.argv
+      |> Array.to_list
+      |> List.filter (fun x -> x <> "")
+      |> Array.of_list
+    in
+    Getopt.parse cmd_specs (fun x -> anon_args := !anon_args @ [x])
+      cmdline 1 (Array.length cmdline -1);
 
-    if show_help () then
+
+    if not no_help && (show_help ()) then
         (help () ; exit 0);
 
+
     (* Check that all mandatory arguments are set *)
     List.filter (fun x -> x.short <> ' ' && x.opt = Mandatory) !specs
     |> List.iter (fun x -> 

ocaml/Command_line.mli

@@ -117,7 +117,7 @@ val help : unit -> unit
 
 (** Sets the specification list as a list of tuples:
     ( short option, long option, documentation, argument ) *)
-val set_specs : description list -> unit
+val set_specs : ?no_help:bool -> description list -> unit
 
 
 (** Returns the list of anonymous arguments *)

ocaml/Input.ml

@@ -788,7 +788,7 @@ end = struct
   let doc = "Type of Jastrow factor [ None | Core | Simple ]"
 
   let of_string s = 
-    match String.capitalize (String.trim  s) with
+    match String.capitalize_ascii (String.trim  s) with
     | "Core" -> Core
     | "Simple" -> Simple
     | "None" -> None

ocaml/Makefile

@@ -24,7 +24,6 @@ ALL_EXE=$(patsubst %.ml,%.native,$(wildcard qp_*.ml)) qmcchem.native
 
 
 default: $(ALL_EXE) 
-	mv qmcchem.native $(QMCCHEM_PATH)/bin/qmcchem
 
 tests: $(ALL_TESTS) 
 

ocaml/Md5.ml

@@ -1,149 +0,0 @@
-open Core
-
-(** Directory containing the list of input files. The directory is created is inexistant. *)
-let input_directory = lazy (
-
-  let ezfio_filename =
-    Lazy.force Qputils.ezfio_filename
-  in
-
-  let dirname = 
-    Filename.concat ezfio_filename "input"
-  in
-
-  begin
-    match ( Sys.is_directory dirname ) with
-    | `No  -> Unix.mkdir  dirname
-    | _    -> ()
-  end ;
-
-  dirname
-)
-
-
-(** List of files responsible for the MD5 key of the input *)
-let files_to_track = [
-  "ao_basis/ao_coef.gz" ;
-  "ao_basis/ao_expo.gz" ;
-  "ao_basis/ao_nucl.gz" ;
-  "ao_basis/ao_num" ; 
-  "ao_basis/ao_power.gz" ;
-  "ao_basis/ao_prim_num.gz" ; 
-  "electrons/elec_alpha_num" ;
-  "electrons/elec_beta_num" ;
-  "electrons/elec_walk_num" ;
-  "jastrow/jast_type" ;
-  "mo_basis/mo_coef.gz" ;
-  "mo_basis/mo_tot_num" ;
-  "nuclei/nucl_charge.gz" ;
-  "nuclei/nucl_coord.gz" ;
-  "nuclei/nucl_num" ;
-  "simulation/ci_threshold" ;
-  "simulation/nucl_fitcusp_factor" ;
-  "simulation/jast_a_up_dn" ;
-  "simulation/jast_a_up_up" ;
-  "simulation/jast_b_up_dn" ;
-  "simulation/jast_b_up_up" ;
-  "simulation/jast_core_a1" ;
-  "simulation/jast_core_a2" ;
-  "simulation/jast_core_b1" ;
-  "simulation/jast_core_b2" ;
-  "simulation/jast_een_e_a.gz" ;
-  "simulation/jast_een_e_b.gz" ;
-  "simulation/jast_een_n.gz" ;
-  "simulation/jast_pen.gz" ;
-  "simulation/method" ;
-  "simulation/time_step" ;
-  "simulation/dmc_projection_time" ;
-  "spindeterminants/bit_kind" ;
-  "spindeterminants/n_det" ;
-  "spindeterminants/n_det_alpha" ;
-  "spindeterminants/n_det_beta" ;
-  "spindeterminants/n_int" ;
-  "spindeterminants/n_states" ;
-  "spindeterminants/psi_coef_matrix_columns.gz" ;
-  "spindeterminants/psi_coef_matrix_rows.gz" ;
-  "spindeterminants/psi_coef_matrix_values.gz" ;
-  "spindeterminants/psi_det_alpha.gz" ;
-  "spindeterminants/psi_det_beta.gz" ;
-  "/pseudo/do_pseudo" ;
-  "/pseudo/mo_pseudo_grid.gz" ;
-  "/pseudo/pseudo_dz_kl.gz";
-  "/pseudo/pseudo_klocmax" ;
-  "/pseudo/pseudo_n_k.gz" ;
-  "/pseudo/pseudo_v_kl.gz" ;
-  "/pseudo/pseudo_grid_rmax" ;
-  "/pseudo/pseudo_kmax" ;
-  "/pseudo/pseudo_n_kl.gz" ;
-  "/pseudo/pseudo_dz_k.gz" ;
-  "/pseudo/pseudo_grid_size" ;
-  "/pseudo/pseudo_v_k.gz" ;
-  ]
-
-
-(** Get an MD5 ke from the content of a file. *)
-let hash_file filename =
-  match Sys.is_file filename with
-  | `Yes -> 
-    begin
-      In_channel.with_file filename ~f:(fun ic ->
-        Cryptokit.hash_channel (Cryptokit.Hash.md5 ()) ic
-        |> Cryptokit.transform_string (Cryptokit.Hexa.encode ()) )
-    end
-  | _ -> ""
-  
-
-(** Cache containing the current value of the MD5 hash. *)
-let _hash = 
-  ref None
-
-(** Get the hash correcponding to the EZFIO file. *)
-let hash () = 
-  let compute_hash () =
-    let ezfio_filename =
-      Lazy.force Qputils.ezfio_filename
-    in
-    let old_md5 =
-      if Ezfio.has_simulation_md5_key () then
-         Ezfio.get_simulation_md5_key ()
-      else
-         ""
-    in
-    let md5_string = 
-      files_to_track
-      |> List.map ~f:(fun x -> Printf.sprintf "%s/%s" ezfio_filename x)
-      |> List.map ~f:hash_file
-      |> String.concat
-    in
-
-    let new_md5 = 
-      md5_string
-      |> Cryptokit.hash_string (Cryptokit.Hash.md5 ()) 
-      |> Cryptokit.transform_string (Cryptokit.Hexa.encode ()) 
-    in
-    if (new_md5 <> old_md5) then
-      begin
-        Printf.eprintf "Info : MD5 key changed\n   %s\n-> %s\n%!" old_md5 new_md5 ;
-        Ezfio.set_simulation_md5_key new_md5
-      end
-    ;
-    new_md5
-  in
-  match (!_hash) with
-  | Some key -> key
-  | None -> 
-      begin
-        let key =
-          compute_hash ()
-        in
-        _hash := Some key ;
-        key
-      end
-
-(** Reset the cache of the MD5 hash. *)
-let reset_hash () =
-  _hash := None;
-  ignore (hash ())
-
-
-

ocaml/QmcMd5.ml

@@ -10,7 +10,7 @@ let input_directory = lazy (
   in
 
   begin
-    if not (Sys.is_directory dirname) then 
+    if not (Sys.file_exists dirname && Sys.is_directory dirname) then 
       Unix.mkdir dirname 0o777
   end ;
 

ocaml/Qmcchem_dataserver.ml

@@ -36,13 +36,12 @@ let run ?(daemon=true) ezfio_filename =
           Printf.printf "Generating initial walkers...\n%!";
           match Unix.fork () with
           | 0 ->
-              Unix.execv
+              Unix.execvp
                 (Lazy.force Qmcchem_config.qmc_create_walkers)
                 [|"qmc_create_walkers" ; ezfio_filename|]
           | pid -> 
               begin
-                let pid', status = Unix.waitpid [] pid in
-                assert (status = Unix.WEXITED 0);
+                ignore @@ Unix.waitpid [] pid;
                 Printf.printf "Initial walkers ready\n%!"
               end
         end 
@@ -348,8 +347,8 @@ let run ?(daemon=true) ezfio_filename =
       Lazy.force Block.dir_name
     in
     let () = 
-      if not (Sys.is_directory dirname) then
-        Unix.mkdir dirname 0o600
+      if not ( Sys.file_exists dirname && Sys.is_directory dirname ) then
+        Unix.mkdir dirname 0o755
     in 
     Filename.concat dirname (
       hostname  ^ "." ^ (string_of_int dataserver_pid)
@@ -393,7 +392,10 @@ let run ?(daemon=true) ezfio_filename =
     Unix.rename block_channel_filename_locked block_channel_filename_tmp;
     Random_variable.compress_files ();
     send_log "status" 0 t0 "Compressed block file";
+    if Sys.file_exists block_channel_filename_locked then
       block_channel := open_out_gen [ Open_append ] 0o660 block_channel_filename_locked
+    else
+      block_channel := open_out block_channel_filename_locked
   in
 
 

ocaml/Qmcchem_edit.ml

@@ -252,12 +252,12 @@ let run ~c ?f ?t ?l ?m ?e ?et ?s ?ts ?w ?wt ?n ?j ?p ?input ezfio_filename =
         Filename.concat (Filename.concat ezfio_filename "blocks") (QmcMd5.hash ()) 
       in
       let rec clean_dir y =
-        if Sys.is_directory y then
+        if Sys.file_exists y && Sys.is_directory y then
           begin
             Sys.readdir y
             |> Array.map (fun x -> Filename.concat y x)
             |> Array.iter (function x ->
-                if Sys.is_directory x  then
+                if Sys.file_exists x && Sys.is_directory x  then
                   clean_dir x
                 else
                   Sys.remove x

ocaml/Qmcchem_forwarder.ml

@@ -48,7 +48,7 @@ let run ezfio_filename dataserver =
    *)
   let () = 
     try
-      Unix.mkdir tmpdir 0o600;
+      Unix.mkdir tmpdir 0o755;
       Unix.chdir tmpdir
     with
     | Unix.Unix_error _ ->
@@ -69,7 +69,7 @@ let run ezfio_filename dataserver =
             | pid ->
                 try
                   Unix.kill pid 0 ;
-                  ignore @@ Unix.execv prog argv
+                  ignore @@ Unix.execvp prog argv
                 with
                 | Unix.Unix_error (Unix.ESRCH, _, _) -> ()
           end

ocaml/Qmcchem_info.ml

@@ -10,7 +10,7 @@ let run ezfio_filename =
     [| qmcchem_info ; ezfio_filename |]
   in
   ignore @@
-    Unix.execv prog argv 
+    Unix.execvp prog argv 
 
 let command () =
   let open Command_line in

ocaml/Qmcchem_result.ml

@@ -224,7 +224,7 @@ let command () =
         doc="Display the convergence of the error of the property by merging blocks";
         arg=With_arg "<string>"; };
     
-      { short='h' ; long="histogram" ; opt=Optional ;
+      { short='i' ; long="histogram" ; opt=Optional ;
         doc="Display the histogram of the property blocks" ;
         arg=With_arg "<string>"; };
     

ocaml/Qmcchem_run.ml

@@ -48,7 +48,6 @@ let full_run ?(start_dataserver=true) ezfio_filename  =
     end;
   
 
-(*
   (* Check if the Zmq Rep socket is open *)
   let test_open_rep_socket () =
     let zmq_context =
@@ -86,7 +85,7 @@ let full_run ?(start_dataserver=true) ezfio_filename  =
   | n  -> 
     if (not (test_open_rep_socket ())) then
       begin
-       Unix.sleepf 0.5;
+       Unix.sleep 2;
        count (n-1);
       end
     else
@@ -94,7 +93,6 @@ let full_run ?(start_dataserver=true) ezfio_filename  =
   in
   if (not (count 300)) then
     Watchdog.kill ();
-  *)
   Unix.sleep 3;
      
 

ocaml/Qputils.ml

@@ -13,7 +13,7 @@ let set_ezfio_filename ezfio_filename =
       failwith (ezfio_filename^" does not exist")
   in
   let () =
-    if Sys.is_directory ezfio_filename then
+    if Sys.file_exists ezfio_filename && Sys.is_directory ezfio_filename then
       Ezfio.set_file ezfio_filename 
     else
       failwith ("Error : "^ezfio_filename^" is not a directory")
@@ -34,13 +34,30 @@ let ezfio_filename = lazy (
     match f with
     | "EZFIO_File" ->
         begin
-          if (Array.length Sys.argv = 1) then
+          let args =
+            Command_line.anon_args ()
+            |> Array.of_list
+          in
+          if (Array.length args < 1) then
              failwith "Error : EZFIO directory not specified on the command line\n";
-          Sys.argv.(1)
+          args.(0)
         end
     | f -> f
   in
   set_ezfio_filename full_path;
+
+  (*
+  (* Check if input directory is present *)
+  let dirname = Filename.concat full_path "input" in
+  if not (Sys.file_exists dirname) then
+    Unix.mkdir dirname 0o755;
+
+  (* Check if blocks directory is present *)
+  let dirname = Filename.concat full_path "blocks" in
+  if not (Sys.file_exists dirname) then
+    Unix.mkdir dirname 0o755;
+    *)
+
   !Ezfio.ezfio_filename
 )
 

ocaml/Random_variable.ml

@@ -681,14 +681,15 @@ let compress_files () =
   let out_channel_dir = 
     let rand_num = Random.int 1000000 |> string_of_int in
     let tmp_dir =
-      Filename.concat "!Ezfio.ezfio_filename" @@
-      Filename.concat "blocks" @@
-      Filename.concat "qmc" rand_num
+      Filename.concat !Ezfio.ezfio_filename @@
+      Filename.concat "blocks" "qmc"^rand_num
     in
     try
-      Unix.mkdir tmp_dir 0o600;
+      Unix.mkdir tmp_dir 0o755;
       tmp_dir
-    with _ -> raise (Sys_error "Cannot create temp dir")
+    with _ ->
+    let message = Printf.sprintf "Cannot create temp dir %s" tmp_dir in
+    raise (Sys_error message)
   in
 
   let out_channel_name = 

ocaml/Time.ml

@@ -10,15 +10,15 @@ let to_sec t =
   sec +
   min  * 60 +
   hour * 60 * 60 + 
-  mday * 60 * 60 * 24 
+  (mday-1) * 60 * 60 * 24 
 
 let string_of_t t = 
-  let mday = t.Unix.tm_mday in
+  let mday = t.Unix.tm_mday - 1 in
   let sec  = t.Unix.tm_sec
   and min  = t.Unix.tm_min
   and hour = t.Unix.tm_hour + 24*mday
   in
-  Printf.sprintf "%2d:%2d:%2d" hour min sec
+  Printf.sprintf "%2d:%2.2d:%2.2d" hour min sec
 
 let string_of_date t = 
   let year = 1900 + t.Unix.tm_year in
@@ -35,7 +35,7 @@ let string_of_date t =
       | 8  -> "Sep" | 9  -> "Oct" | 10 -> "Nov" | 11 -> "Dec"
       | _ -> assert false
   in
-  Printf.sprintf "%2d %3s %4d - %2.2d:%2.2d:%2.2d" mday month year hour min sec
+  Printf.sprintf "%2d %3s %4d - %2d:%2.2d:%2.2d" mday month year hour min sec
 
 
 let string_of_now () = 

ocaml/Watchdog.ml

@@ -1,16 +1,16 @@
-let _list    = ref [] ;;
-let _running = ref false;;
-let _threads = ref [] ;;
+let _list    = ref [] 
+let _running = ref false
+let _threads = ref [] 
 
 (** Kill the current process and all children *)
 let kill () =
   let kill pid = 
-    Unix.kill pid Sys.sigint;
+    Unix.kill pid Sys.sigkill;
     Printf.printf "Killed %d\n%!" pid
   in
   List.iter kill (!_list);
   exit 1 
-;;
+
 
 
 (** Start watchdog *)
@@ -50,7 +50,7 @@ let start () =
       in
       _threads := ( (Thread.create f) () ) :: (!_threads)
     end
-;;
+
 
 (** Stop watchdog *)
 let stop () =
@@ -58,14 +58,14 @@ let stop () =
     _running := false
   else
     failwith "Watchdog error: Already stopped"
-;;
+
 
 (** Add a PID to tracking *)
 let add pid = 
   if (not !_running) then
     start ();
   _list := pid :: (!_list)
-;;
+
 
 (** Remove a PID from tracking *)
 let del pid = 
@@ -82,14 +82,13 @@ let del pid =
   match (!_list) with
   | [] -> if (!_running) then stop ()
   | _ -> ()
-;;
+
 
 (** Fork and exec a new process *)
 let fork_exec ~prog ~args () =
   let pid = 
     match Unix.fork () with
-    | 0 -> (* Chile process *)
-        let _ = Unix.execv prog args in 0
+    | 0 -> Unix.execvp prog args 
     | pid -> pid
   in
 
@@ -111,11 +110,11 @@ let fork_exec ~prog ~args () =
   in
   _threads := ( (Thread.create f) () ) :: (!_threads);
   pid
-;;
+
 
 (** Wait for threads to finish *)
 let join () =
 (*  if (!_running) then stop (); *)
   List.iter Thread.join (!_threads);
   assert (not !_running)
-;;
+

ocaml/qmcchem.ml

@@ -1,27 +1,51 @@
 let update_command_line () =
   let last = (Array.length Sys.argv) - 2 in
-  Sys.argv.(0) <- Sys.argv.(0) ^ " " ^ Sys.argv.(1);
+  Sys.argv.(0) <- Sys.argv.(0) ^ "_" ^ Sys.argv.(1);
   for i=1 to last do
     Sys.argv.(i) <- Sys.argv.(i+1)
   done;
-  Sys.argv.(last+1) <- "--"
+  Sys.argv.(last+1) <- ""
 
 
+let help () = 
+  Printf.printf "
+qmcchem - QMC=Chem command 
+
+Usage:
+  
+  qmcchem [-h] COMMAND
+  
+Arguments:
+  
+  COMMAND       QMC=Chem command to run :
+                [run|edit|stop|result|md5|info|debug] 
+  
+Options:
+  
+  -h  --help    Prints the help message. 
+  
+Description:
+  
+  Driver for subcommands. 
+
+"
 
 let () =
-  let open Command_line in
-  begin
-    set_header_doc (Sys.argv.(0) ^ " - QMC=Chem command");
-    set_description_doc "Driver for subcommands.";
-    set_specs []
-  end; 
-
   if Array.length Sys.argv < 2 then
-    (Command_line.help (); failwith "Inconsistent command line");
+    (help (); failwith "Inconsistent command line") ;
   
-  let command = Sys.argv.(1) in
+  match String.trim Sys.argv.(1) with
+  | "-h" | "--help" -> 
+    begin
+      help () ;
+      exit 0
+    end
+  | _ -> 
+    begin
+      let command =
+        Sys.argv.(1)
+      in
       update_command_line ();
-  Command_line.reset ();
 
       match command with
       | "debug"  -> let open Qmcchem_debug  in command ()
@@ -31,6 +55,6 @@ let () =
       | "result" -> let open Qmcchem_result in command ()
       | "run"    -> let open Qmcchem_run    in command ()
       | "stop"   -> let open Qmcchem_stop   in command ()
-  | _        -> (Command_line.help () ; failwith "Inconsistent command line")
-
+      | _        -> (help () ; failwith "Inconsistent command line")
+    end
 

ocaml/qptypes_generator.ml

@@ -296,7 +296,7 @@ let input_lines filename =
 let create_ezfio_handler () =
   let lines = 
     input_lines "ezfio.ml"
-    |> List.mapi (fun i l -> if i > 470 then Some l else None)
+    |> List.mapi (fun i l -> if i > 474 then Some l else None)
     |> List.filter (fun x -> x <> None)
     |> List.map (fun x ->
         match x with

scripts/clean.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 # This script is supposed to run in $QMCCHEM_PATH
 
-ninja -C ocaml clean 
+make -C ocaml clean 
 if [[ -d src/IRPF90_temp ]]
 then
   ninja -C src/IRPF90_temp -t clean 

scripts/compile_ocaml.sh

@@ -8,4 +8,4 @@ fi
 
 cd ${QMCCHEM_PATH}/ocaml || exit -1
 
-exec ninja -f generated.ninja ${@} || exit -1
+exec make

src/ezfio_interface.irp.f

@@ -52,7 +52,7 @@ data = [ \
 ]
 
 data_no_set = [\
-("mo_basis_mo_tot_num"     ,  "integer"           ,  ""),
+("mo_basis_mo_num"     ,  "integer"           ,  ""),
 ("pseudo_ao_pseudo_grid"   ,  "double precision"  ,  "(ao_num,pseudo_lmax+pseudo_lmax+1,pseudo_lmax-0+1,nucl_num,pseudo_grid_size)"),
 ("pseudo_mo_pseudo_grid"   ,  "double precision"  ,  "(ao_num,pseudo_lmax+pseudo_lmax+1,pseudo_lmax-0+1,nucl_num,pseudo_grid_size)"),
 ("pseudo_pseudo_dz_k"      ,  "double precision"  ,  "(nucl_num,pseudo_klocmax)"),

src/mo.irp.f

@@ -410,7 +410,7 @@ BEGIN_PROVIDER [ integer, mo_tot_num ]
   END_DOC
   
   mo_tot_num = -1
-  call get_mo_basis_mo_tot_num(mo_tot_num)
+  call get_mo_basis_mo_num(mo_tot_num)
   if (mo_tot_num <= 0) then
     call abrt(irp_here,'Total number of MOs can''t be <0')
   endif