Evaluating a mathematica notebook via the command line and saving the evaluated file

Question

I am attempting to evaluate a notebook with the following code via the command line

Z = PauliMatrix[3];
X = PauliMatrix[1];
Y = PauliMatrix[2];
id = PauliMatrix[0];
spinRaise = (X + I Y)/2;
spinLower = (X - I Y)/2;
pauli0 = 1/2 (id - (Z/(2 + 1)));
zero = {1, 0};
one = {0, 1};
\[Sigma]p = (1/2) (X + I Y);
\[Sigma]m = (1/2) (X - I Y);
\[Sigma]0 = (1/2) (id - Z/(2 n + 1));
\[Sigma]z = {{1, 0}, {0, -1}};

fragState = {{1/2, 1/2}, {1/2, 1/2}};
\[Rho]initialE = KroneckerProduct[fragState, fragState, fragState];
(*systemInitial={{1/4,1/4,0,0},{1/4,1/4,0,0},{0,0,0,0},{0,0,0,1/2}}*)

systemInitial = {{1/2, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 1/4, 1/4}, {0, 
    0, 1/4, 1/4}};
(*systemInitial={{1/2,0,0,0},{0,0,0,0},{0,0,0,0},{0,0,0,1/2}};*)
\
(*systemInitial={{1/3,0,0,0},{0,0,0,0},{0,0,1/3,1/3},{0,0,1/3,1/3}};*)

totalSysInitial = 
  KroneckerProduct[N[systemInitial], N[\[Rho]initialE]];
subsystem2Measure1 = 
  KroneckerProduct[{Cos[\[Theta]], Exp[I \[Phi]]*Sin[\[Theta]]}, 
   Conjugate[{Cos[\[Theta]], Exp[I \[Phi]]*Sin[\[Theta]]}]];
subsystem2Measure2 = 
  KroneckerProduct[{Exp[-I \[Phi]]*Sin[\[Theta]], -Cos[\[Theta]]}, 
   Conjugate[{Exp[-I \[Phi]]*Sin[\[Theta]], -Cos[\[Theta]]}]];
postMeasuredState1 = 
  dTraceSystem[
   Flatten[Map[
      KroneckerProduct @@ # &, {{subsystem2Measure1, 
        IdentityMatrix[2]}}], 1].systemInitial.Flatten[
     Map[KroneckerProduct @@ # &, {{subsystem2Measure1, 
        IdentityMatrix[2]}}], 1], {1}, 2];
postMeasuredState2 = 
  dTraceSystem[
   Flatten[Map[
      KroneckerProduct @@ # &, {{subsystem2Measure2, 
        IdentityMatrix[2]}}], 1].systemInitial.Flatten[
     Map[KroneckerProduct @@ # &, {{subsystem2Measure2, 
        IdentityMatrix[2]}}], 1], {1}, 2];
probMeasure1 = 
  Simplify[ComplexExpand[
    Tr[Flatten[
       Map[KroneckerProduct @@ # &, {{postMeasuredState1, 
          IdentityMatrix[2]}}], 1].systemInitial.Flatten[
       Map[KroneckerProduct @@ # &, {{postMeasuredState1, 
          IdentityMatrix[2]}}], 1]]]];
probMeasure2 = 
  Simplify[ComplexExpand[
    Tr[Flatten[
       Map[KroneckerProduct @@ # &, {{postMeasuredState2, 
          IdentityMatrix[2]}}], 1].systemInitial.Flatten[
       Map[KroneckerProduct @@ # &, {{postMeasuredState2, 
          IdentityMatrix[2]}}], 1]]]];
normPost1 = postMeasuredState1/probMeasure1;
normPost2 = postMeasuredState2/probMeasure2;
eigPost1 = 
  Eigenvalues[normPost1 + 10^-15 IdentityMatrix[Length[normPost1]]];
entropyPost1 = 
  Simplify[ComplexExpand[-Sum[
      eigPost1[[j]] Log[2, eigPost1[[j]]], {j, 1, Length[eigPost1]}]]];
eigPost2 = 
  Eigenvalues[normPost2 + 10^-15 IdentityMatrix[Length[normPost2]]];
entropyPost2 = 
  Simplify[ComplexExpand[-Sum[
      eigPost2[[j]] Log[2, eigPost2[[j]]], {j, 1, Length[eigPost2]}]]];
eigSub2 = 
 Eigenvalues[
  dTraceSystem[sysInitial, {1}, 2] + 
   10^-15 IdentityMatrix[Length[dTraceSystem[sysInitial, {1}, 2]]]]
entropyPost2 = 
  Simplify[ComplexExpand[-Sum[
      eigSub2[[j]] Log[2, eigSub2[[j]]], {j, 1, Length[eigSub2]}]]];
entropyPost2 - 
 NMinimize[{probMeasure1*entropyPost1 + 
    probMeasure2*entropyPost2, {\[Theta] \[Element] Reals, \[Theta] <=
      2*\[Pi], \[Phi] \[Element] Reals, 
    0 <= \[Phi] <= 2*\[Pi]}}, {\[Theta], \[Phi]}]

I have tried math -script <notebook.nb, math -run < notebook.nb, the same again using a .wls file instead (yes, I changed the cells to initialisation cells), and also a .m file with math -run "<<notebook.m". Even changed the cells from Input to Code, per this post. There is no change to the files in any of these cases, and the runtime doesn't seem to be what it should be either. Sometime it's instant, others a few seconds. The only one that actually appears to output something to the command line, not even the file, is math -run < notebook.nb

All I want to do is take the notebook file, evaluate it via the command line, and have those evaluations appear in the notebook. I have looked at a myriad of posts, including this one, but I can't get it to work.

Answer 1

The alternative version posted here works fine on Windows, on Mathematica 11.2 at least.

It's somewhat elaborate but it runs the notebook visibly so you can see it executing. The output cells are saved in the notebook.

A batch file runs a kernel which opens, runs & saves a notebook. The initial kernel monitors the notebook execution, useful for batch applications. This means the notebook requires a second kernel, in this case called "Kernel2", created via Kernel Configuration Options as a one-time manual setup. Kernel2 needs to be the notebook kernel, as indicated below. The batch file can be run from the command line or by the Windows Task Scheduler.

The above demo files are zipped and can be extracted from the image below. The files are preconfigured to run from C:\yourPath\

Zip retrieval

extractZip[file_String] := Uncompress@Last@StringSplit[
    URLFetch@file, "Embedded Zip:"]

writeZip[png_String, zip_String] := Module[{},
  outputstream = OpenWrite[FileNameJoin[{$InitialDirectory, zip}],
    BinaryFormat -> True];
  BinaryWrite[outputstream, extractZip@png];
  Close[outputstream]]

writeZip["https://i.stack.imgur.com/H5o8g.png", "files.zip"]

extractZip c/o Simon Woods

For batch runs

Using the same principles, there is also a very robust, albeit slow, batch runner here. Each notebook runs in its own session, and if a notebook hangs its slot will time-out and the next one will be processed. Great for overnight runs.

writeZip["https://i.stack.imgur.com/c2zhD.png", "batchdemo.zip"]

Zip attachment code, for completeness

attachCode[file_String, expr_] := Block[{stream},
  stream = OpenAppend[file];
  WriteString[stream, "Embedded Zip:", Compress@expr];
  Close[stream]]

inputstream = OpenRead["C:\\temp\\batchdemo.zip", BinaryFormat -> True];
data = BinaryReadList[inputstream];
Close[inputstream];
attachCode["H:\\batchdemo.png", data]