### A methodical approach

It will help to have three windows. One to stay in an editor and modify and save "temp.mod". Another to run "modlunit temp" and see the error message. A third to run the UNIX units command to help you figure out certain dimensional factors. What follows assumes steps 0 and 1 have been completed and no other changes have been made to the temp.mod file. The "modlunit temp" output is:

    Checking units of temp.mod
    REACTION quantity units for pump is: 1-21 /m2
    but the quantity units of the first term is: 1-09 /m2
    Inconsistent material quantity units
    Need a correct COMPARTMENT statement at line 52 in file temp.mod
            ~ cam + pump <-> capump ((1e7)*k1, (1e10)*k2<>)

Use the units command to verify that the quantity units of cam are

    you have: micro micron / liter
    you want:
    conformability
            1.000000e-09 /m2
            1.000000e+00

as stated by the modlunit output. We can figure out the right units factor in the COMPARTMENT statement for pump by

    you have: pico/cm2
    you want: micro micron / liter
            * 1.000000e+01
            / 1.000000e-01

and changing the factor (1e12) currently there to (1e1) or (10).

I leave it to the philosophers to explain why something that is measured in moles/cm2 and has a huge factor of (1e13) gets its factor reduced to (1e1) when the units are the much smaller picomoles/cm2. Seems to me the factor should have gone up to (1e25)!

Re-run modlunit. Now it is the flux values that are bad.

    Flux units for this reaction: 1-06 /m2-sec
    This implies forward rate units: 100000 m3/sec
    But the users forward rate units are: 1-07 m3/sec
    inconsistent reaction units at line 52 in file temp.mod
            ~ cam + pump <-> capump ((1e7)*k1, (1e10)*k2<>)

The forward rate factor needs to be changed from 1e7 to 1e-5. That is, since the ratio between user and the implied is 1e-7/1e5 we either multiply or divide the existing factor by this amount. More laboriously we can use the units command again to compare vol* dcam/dt and k1*cam*pump (i.e. micron * uM/ms and /mM-s * uM * pmol/cm2) to see

    you have: liter micro pico / milli s liter cm2
    you want: micro micron/liter ms
            * 1.000000e-05
            / 1.000000e+05

The difficulty in using the UNIX units command is that it requires all terms in the numerator to be written first followed by all the terms in the denominator. I have ordered them so that everything in the numerator for k1 is followed by the numerator for cam followed by the numerator for pump and then the denominator terms respectively.

Now the backward rates are inconsistent and need to be changed from (1e10) to (1e-2). At last, that reaction is dimensionally consistent. Several modlunit runs later we also get the other pump reaction consistent with

            ~ capump <-> cao + pump ((1e-2)*k3, (1e-2)*k4)

When comparing factors to the previous reaction note that cam and cao have different units.

Dimensional problems with expressions are easy to fix since the modlunit command suggests the correct factor. e.g.

    The previous primary expression with units: 1-21 /m2
    is missing a conversion factor and should read:
      (1e-12)*()
     at line 58 in file temp.mod
            CONSERVE pump + capump = (1e13)*pump0<>

can be fixed by writing

            CONSERVE pump + capump = (1e1)*pump0

With this, modlunit no longer complains.

NEURON hands-on course
Copyright © 1998, 1999 by N.T. Carnevale and M.L. Hines, all rights reserved.