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MJ_DFT_Complete.mw
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MJ_DFT_Complete.mw
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<?xml version="1.0" encoding="UTF-8"?>
<Worksheet>
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<Input><Text-field style="Text" layout="Normal">
<Font size="18" bold="true">Input Section: For standard transport calculations these are the only sections that you need to edit. Here you can change the geometry file, work directory, job name, basis set, DFT convergence tolerance, max # of processors that Maple can use, and Megabytes of RAM requested. See Maple Help >> Toolboxes >> Quantum Chemistry >> Basis for a complete list of available basis sets.
</Font></Text-field>
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<Input><Text-field style="Text" layout="Normal"><Font size="20" bold="true">***New Features: A complete transport calculation from starting geometry to final transmission/current calculation!****</Font></Text-field>
</Input>
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<Input><Text-field style="Text" layout="Normal"></Text-field>
</Input>
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<Input><Text-field style="Text" layout="Normal"><Font size="18" underline="true" bold="true" foreground="[255,0,0]">Make sure to align your junction along the x-axis and sort the atoms by x coordinate before you start! You must do this with an external editor like Chem3D, Avogadro, or MoleMod. </Font><Equation executable="true" style="2D Math" input-equation="" display="LUklbXJvd0c2Iy9JK21vZHVsZW5hbWVHNiJJLFR5cGVzZXR0aW5nR0koX3N5c2xpYkdGJzYoLUkjbWlHRiQ2I1EhRictSSdtc3BhY2VHRiQ2Ji8lJ2hlaWdodEdRJjAuMGV4RicvJSZ3aWR0aEdRJjAuMGVtRicvJSZkZXB0aEdGNC8lKmxpbmVicmVha0dRKG5ld2xpbmVGJ0YrLyUlc2l6ZUdRIzE4RicvJSp1bmRlcmxpbmVHUSV0cnVlRicvJSxtYXRodmFyaWFudEdRJ25vcm1hbEYn">LUklbXJvd0c2Iy9JK21vZHVsZW5hbWVHNiJJLFR5cGVzZXR0aW5nR0koX3N5c2xpYkdGJzYoLUkjbWlHRiQ2I1EhRictSSdtc3BhY2VHRiQ2Ji8lJ2hlaWdodEdRJjAuMGV4RicvJSZ3aWR0aEdRJjAuMGVtRicvJSZkZXB0aEdGNC8lKmxpbmVicmVha0dRKG5ld2xpbmVGJ0YrLyUlc2l6ZUdRIzE4RicvJSp1bmRlcmxpbmVHUSV0cnVlRicvJSxtYXRodmFyaWFudEdRJ25vcm1hbEYn</Equation></Text-field>
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<Input><Text-field style="Text" layout="Normal"><Font size="18" bold="true">
<Font foreground="[255,0,0]">#Stuff to Edit for Each Electronic Structure Calculation. </Font></Font></Text-field>
</Input>
</Group></Presentation-Block><Presentation-Block>
<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L266" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"><Font style="Maple Input">molecule := ReadXYZ("alcal.xyz");
dir := "";
filename := "sample_dft";
basis_set := "lanl2dz";
functional := "PBE0";
req_RAM := 60000;
</Font></Text-field>
</Input>
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<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L91" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"></Text-field>
</Input>
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<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L93" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"></Text-field>
</Input>
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<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L272" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"></Text-field>
</Input>
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<Input><Text-field style="Text" layout="Normal"><Font style="Maple Input">
</Font><Font size="18" bold="true" foreground="[255,0,0]">#New Feature: Settings for the NEGF transport calculation. The default settings assume 2 linear electrodes of 3 gold atoms each with 1 gold atom in each electrode being included the transport region (electrode_atoms=2). </Font><Font style="Maple Input">
</Font></Text-field>
</Input>
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<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L302" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"></Text-field>
</Input>
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<Input><Text-field style="Text" layout="Normal"></Text-field>
</Input>
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<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L296" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"><Font style="Maple Input">
<Font size="14" bold="false" foreground="[0,0,0]" family="Lucida Bright">#Settings for the electrodes, calculation type, and temperature*Boltzmann constant.</Font><Font foreground="[0,0,0]" family="Lucida Bright">
</Font>electrode_atoms:= 1;
</Font></Text-field>
</Input>
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<Input><Text-field style="Text" layout="Normal"></Text-field>
</Input>
</Group>
<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L282" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"><Font style="Maple Input">negf_type := "transmission";
kT:=1.07E-09;
</Font><Font size="14" family="Lucida Bright" executable="true">#These set the electrode Fermi level/electron density (Metal/shape dependent)</Font><Font style="Maple Input" bold="false" foreground="[0,0,0]" family="Lucida Bright">
</Font><Font style="Maple Input">Fermi_level_leftelec := -4.4;
Fermi_level_rightelec := -4.4;
LeftElectrode_electron_density :=0.07;
RightElectrode_electron_density :=0.07;<Font bold="false">
</Font></Font><Font size="14" family="Lucida Bright" executable="true">#These settings determine the transmission and voltage range for the calculation. Important: delta_energy should be less than or equal to delta_volts for current calculations. Voltage is only used for current calculations.
</Font><Font style="Maple Input">FermiWindow_min:=-15.5;
FermiWindow_max:=5.5;
delta_energy:=0.1;
Min_voltage:=0;
Max_voltage:=1;
delta_volts:=0.1;
</Font></Text-field>
</Input>
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<Input><Text-field style="Text" layout="Normal"><Font style="Maple Input">
</Font><Font size="18" bold="true" foreground="[255,0,0]" family="Lucida Bright">#Stuff to Edit if Needed (Problem Dependent). </Font><Font style="Maple Input" family="Lucida Bright">
</Font></Text-field>
</Input>
</Group>
<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L260" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"></Text-field>
</Input>
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<Input><Text-field style="Text" layout="Normal"><Font style="Maple Input" family="Lucida Bright">
</Font></Text-field>
</Input>
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<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L264" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"></Text-field>
</Input>
</Group>
<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L95" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"><Font style="Maple Input">dft_conv := 1E-5;
num_cpus := 4;
exe_name := "RUQT_v1r.x";
output_ext := ".negf";</Font></Text-field>
</Input>
</Group>
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<Input><Text-field style="Text" layout="Normal"><Font style="Maple Input">
</Font></Text-field>
</Input>
</Group></Presentation-Block><Presentation-Block>
<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L97" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"><Font size="18" bold="true" foreground="[255,0,0]" family="Lucida Bright">#Directions For Running Calculations</Font></Text-field>
</Input>
</Group></Presentation-Block><Presentation-Block>
<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L18" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"><Font size="14" bold="true">
To run the calculation, simply export this file as a .mpl script by:</Font></Text-field>
</Input>
</Group></Presentation-Block><Presentation-Block>
<Group view="presentation" inline-output="false" labelreference="L19" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" size="14" layout="Normal"></Text-field>
</Input>
</Group></Presentation-Block><Presentation-Block>
<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L21" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" size="14" layout="Normal"><Font size="14" bold="true">1. Going to File>>Export As...
2. Choose Maple input (.mpl)</Font></Text-field>
</Input>
</Group></Presentation-Block><Presentation-Block>
<Group view="presentation" inline-output="false" labelreference="L26" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" size="14" layout="Normal"><Font size="14" bold="true">3. Save the script to your work directory</Font></Text-field>
</Input>
</Group></Presentation-Block><Presentation-Block>
<Group view="presentation" inline-output="false" labelreference="L24" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" size="14" layout="Normal"></Text-field>
</Input>
</Group></Presentation-Block><Presentation-Block>
<Group view="presentation" inline-output="false" labelreference="L25" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" size="14" layout="Normal"><Font size="14" bold="true">Once you have your script.mpl, you can run it in your terminal and output the results to a file of your choosing by using the following command line input:
</Font><Font size="20" bold="true">maple script.mpl &> output_file &</Font></Text-field>
</Input>
</Group></Presentation-Block><Presentation-Block>
<Group view="presentation" inline-output="false" labelreference="L27" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" size="14" layout="Normal"></Text-field>
</Input>
</Group></Presentation-Block><Presentation-Block>
<Group view="presentation" inline-output="false" labelreference="L28" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" size="14" layout="Normal"><Font size="14" bold="true">Make to include the & and > and NO SPACES in the filenames! Linux does not like spaces in file or directory names. Use underscores (_) instead. To Linux, a space means that you are giving it two different commands or filenames ("xmaple test_1.mw" is 1 command and 1 filename but "xmaple test 1.mw" is 1 command and 2 filenames).
</Font></Text-field>
</Input>
</Group></Presentation-Block><Presentation-Block>
<Group view="presentation" hide-input="false" hide-output="false" inline-output="false" labelreference="L234" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"><Font size="14" bold="true">This version of the worksheet runs only a Density Functional calculation and generates an .scf_dat file. This does not run any p2-RDM or Hartree-Fock calculations.
This calculation also produces a .orb_dat file which contains orbital data that you need to make the NEGF input separately.</Font></Text-field>
</Input>
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<Group view="presentation" inline-output="false" labelreference="L293" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"></Text-field>
</Input>
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<Group view="presentation" inline-output="false" labelreference="L292" drawlabel="true" applyint="true" applyrational="true" applyexponent="false">
<Input><Text-field style="Text" layout="Normal"><Font size="14" bold="true" foreground="[255,0,0]">
</Font><Font size="18" bold="true" foreground="[255,0,0]">#MAPLE CODE BELOW. EDIT ONLY AS NEEDED/DIRECTED. </Font><Font size="18" bold="true">
</Font></Text-field>
</Input>
</Group></Presentation-Block><Presentation-Block><CodeEditor-ExecGroup view="presentation" hide-input="false" inline-output="false" labelreference="L307" drawlabel="true" applyint="true" applyrational="true" display="code"><EC-CodeEditor id="CodeEditRegion0" expanded="false" visible="true" pixel-width="500" pixel-height="200" code-language="text/maple" autofit="true" wrapping="true" show-border="true" code-line-numbers="true">
#Calculation Section: This part runs the DFT calculations. For standard NEGF calculations, you will not need to edit this part.
kernelopts(numcpus=num_cpus):
dft_results := DensityFunctional(molecule, xc=functional, basis = basis_set, symmetry = false, max_memory = req_RAM, conv_tol = dft_conv, max_cycle = 400);
hf_data := MOIntegrals(molecule, method = 'DensityFunctional', xc=functional, basis = basis_set, symmetry = false, max_memory = req_RAM, conv_tol = dft_conv, max_cycle = 400):
dft_ener := dft_results[e_tot];
#This part puts the DFT data (Orbital and Hamiltonian data) into a the .scf_dat and .orb_dat files. Do not change this part without direction or the NEGF code may not work. It now also creates the NEGF input and runs the transport calculation.
num_orb := Size(dft_results[mo_occ], 1):
num_occ := rtable_num_elems(dft_results[mo_occ],NonZero):
num_virt := num_orb - num_occ:
atomic_overlap := Array(1 .. num_orb, 1 .. num_orb, datatype = float[8]):
temp_s2 := Array(1 .. num_orb, 1 .. num_orb, datatype = float[8]):
temp_s := Array(1 .. num_orb, 1 .. num_orb, datatype = float[8]):
e_mat := Array(diagonal, 1 .. num_orb, 1 .. num_orb, datatype = float[8]):
for i to num_orb do
e_mat[i, i] := dft_results[mo_energy][i]:
end do:
inv_mc := MatrixInverse(dft_results[mo_coeff]):
for i to num_orb do for j to num_orb do for a to num_orb do
temp := inv_mc[a, i]*hf_data[overlap_integrals][a, j]; temp_s2[i, j] := temp_s2[i, j] + temp;
end do; end do; end do;
for i to num_orb do for j to num_orb do for a to num_orb do
temp := inv_mc[a, i]*temp_s2[j, a]; atomic_overlap[i, j] := atomic_overlap[i, j] + temp;
end do; end do; end do;
temp_s := MatrixMatrixMultiply(e_mat, inv_mc):
temp_s2 := MatrixMatrixMultiply(dft_results[mo_coeff], temp_s):
Fock_mat := MatrixMatrixMultiply(atomic_overlap, temp_s2):
fd := fopen(cat(dir, filename, ".scf_dat"), WRITE):
fprintf(fd, "%s\134n", "Molecular Orbital Coefficients"):
for x to num_orb do for y to num_orb do
fprintf(fd, "%d%c%d%c%.16e\134n", x, " ", y, " ", dft_results[mo_coeff][x, y])
end do end do:
fprintf(fd, "%s\134n", "Molecular Orbital Energies"):
for x to num_orb do
fprintf(fd, "%d%c%.16e\134n", x, " ", dft_results[mo_energy][x])
end do:
fprintf(fd, "%s\134n", "Overlap Matrix"):
for x to num_orb do for y to num_orb do
fprintf(fd, "%d%c%d%c%.16e\134n", x, " ", y, " ", atomic_overlap[x, y])
end do end do:
fprintf(fd, "%s\134n", "Fock Matrix"):
for x to num_orb do for y to num_orb do
fprintf(fd, "%d%c%d%c%.16e\134n", x, " ", y, " ", Fock_mat[x, y])
end do end do:
fclose(fd):
num_leftelec := 0:
atom_num := 0:
for x to num_orb while atom_num < electrode_atoms do
ao_label := sscanf(dft_results[aolabels][x], "%d%s%s"):
num_leftelec := num_leftelec + 1:
atom_num := ao_label[1]:
end do:
num_leftelec := num_leftelec - 1:
num_trans := num_orb - 2*num_leftelec:
fd2 := fopen(cat(dir, filename, ".orb_dat"), WRITE):
fprintf(fd2, "%s\134n", "Orbital Numbers for NEGF Transport Calculations"):
fprintf(fd2, "%s%s\134n", "Basis Set Used: ", basis_set):
fprintf(fd2, "%s%d\134n", "Total Orbitals: ", num_orb):
fprintf(fd2, "%s%d\134n", "Occupied Orbitals: ", num_occ):
fprintf(fd2, "%s%d\134n", "Unoccupied(Virtual) Orbitals: ", num_virt):
fprintf(fd2, "%s%d\134n", "Orbitals in Left Electrode(size_l): ", num_leftelec):
fprintf(fd2, "%s%d\134n", "Orbitals in Transport Region(size_c): ", num_trans):
fprintf(fd2, "%s%d\134n", "Orbitals in Right Electrode(size_r): ", num_leftelec):
fprintf(fd2, "%s\134n", ""):
fprintf(fd2, "%s\134n", "Atomic Orbital Labels & Populations from Atom 0"):
for x to num_orb do
fprintf(fd2, "%s%c%f\134n", dft_results[aolabels][x]," ",dft_results[populations][x])
end do:
fclose(fd2):
fd3 := fopen(cat(dir, filename), WRITE):
fprintf(fd3, "%s\134n", negf_type):
fprintf(fd3, "%s\134n", "Metal_WBL"):
fprintf(fd3, "%f\134n", Fermi_level_leftelec):
fprintf(fd3, "%f\134n", Fermi_level_rightelec):
fprintf(fd3, "%f\134n", LeftElectrode_electron_density):
fprintf(fd3, "%f\134n", RightElectrode_electron_density):
fprintf(fd3, "%d\134n", num_orb):
fprintf(fd3, "%d\134n", num_orb):
fprintf(fd3, "%d\134n", 0):
fprintf(fd3, "%d\134n", 0):
fprintf(fd3, "%d\134n", num_occ):
fprintf(fd3, "%d\134n", num_virt):
fprintf(fd3, "%d\134n", num_trans):
fprintf(fd3, "%d\134n", num_leftelec):
fprintf(fd3, "%d\134n", num_leftelec):
fprintf(fd3, "%f\134n", FermiWindow_min):
fprintf(fd3, "%f\134n", FermiWindow_max):
fprintf(fd3, "%f\134n", delta_energy):
fprintf(fd3, "%f\134n", Min_voltage):
fprintf(fd3, "%f\134n", Max_voltage):
fprintf(fd3, "%f\134n", delta_volts):
fprintf(fd3, "%.16E\134n", kT):
fprintf(fd3, "%s\134n", "maple"):
fprintf(fd3, "%s\134n", "F"):
fprintf(fd3, "%s\134n", "dft"):
fprintf(fd3, "%s\134n", "F"):
fprintf(fd3, "%s\134n", "M"):
fprintf(fd3, "%s\134n", "F"):
fprintf(fd3, "%d\134n", 1):
fclose(fd3):
#This part runs the transport calculation! Returns both a .dat and a .output_ext file.
negf_calc:=system(cat(exe_name," ",dir,filename," &> ",filename,output_ext," &"));
if (negf_calc=0) then
fd4:=fopen(cat(dir, filename, ".dat"), READ):
else printf("Your NEGF calculation failed. Check your output.negf file");
end if:
if (negf_calc=0) then
if (negf_type="transmission") then
printf("Plotting Transmission vs Energy (eV)");
elif (negf_type="current") then
printf("Plotting Current (Amps) vs Voltage (V)");
end if;
readline(fd4):
coord := readdata(fd4, 2):
fclose(fd4):
end if:
if (negf_calc=0) then
negf_plot:=plot(coord,style=pointline,color="NavyBlue");
end if;
if (negf_calc=0) then
exportplot(cat(dir, filename, ".jpeg"),negf_plot):
end if:</EC-CodeEditor></CodeEditor-ExecGroup></Presentation-Block><Presentation-Block>
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