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It would have been helpful to see a graph showin the discrepancy.

Anwyways, from a cursory look I'd say your Output:Variable is wrong. Here's what you have:

Output:Variable,
    *,                       !- Key Value
    Schedule Value,          !- Variable Name
    Timestep,                !- Reporting Frequency
    MiscElecLoad_1;          !- Schedule Name

I suspect you don't understand what Schedule Name actually does. See the I/O Reference Guide, but in short:

The output variable will be active during any hour in which the schedule value is >0

If you want to report only one schedule named MiscElecLoad_1 you should do it like so:

Output:Variable,
    MiscElecLoad_1,          !- Key Value
    Schedule Value,          !- Variable Name
    Timestep;                !- Reporting Frequency

It would have been helpful to see a graph showin the discrepancy.

Anwyways, from a cursory look I'd say your Output:Variable is wrong. Here's what you have:

Output:Variable,
    *,                       !- Key Value
    Schedule Value,          !- Variable Name
    Timestep,                !- Reporting Frequency
    MiscElecLoad_1;          !- Schedule Name

I suspect you don't understand what Schedule Name Schedule Name actually does. See the I/O Reference Guide, but in short:

The output variable will be active during any hour in which the schedule value is >0

If you want to report only one schedule named MiscElecLoad_1 you should do it like so:

Output:Variable,
    MiscElecLoad_1,          !- Key Value
    Schedule Value,          !- Variable Name
    Timestep;                !- Reporting Frequency

It would have been helpful to see a graph showin the discrepancy.

Anwyways, from a cursory look I'd say your Output:Variable is wrong. Here's what you have:

Output:Variable,
    *,                       !- Key Value
    Schedule Value,          !- Variable Name
    Timestep,                !- Reporting Frequency
    MiscElecLoad_1;          !- Schedule Name

I suspect you don't understand what Schedule Name actually does. See the I/O Reference Guide, but in short:

The output variable will be active during any hour in which the schedule value is >0

If you want to report only one schedule named MiscElecLoad_1 you should do it like so:

Output:Variable,
    MiscElecLoad_1,          !- Key Value
    Schedule Value,          !- Variable Name
    Timestep;                !- Reporting Frequency

2005-06-12 23:32:00    0.0
2005-06-12 23:33:00    0.0
2005-06-12 23:34:00    0.0
2005-06-12 23:35:00    0.0
2005-06-12 23:36:00    0.0
2005-06-12 23:37:00    0.0

It (It would have been helpful to see a graph showin the discrepancy.

Anwyways, showing the discrepancy).

Anyways, from a cursory look I'd say your Output:Variable Output:Variable is wrong. Here's what you have:

Output:Variable,
    *,                       !- Key Value
    Schedule Value,          !- Variable Name
    Timestep,                !- Reporting Frequency
    MiscElecLoad_1;          !- Schedule Name

I suspect you don't understand what Schedule Name actually does. See the I/O Reference Guide, but in short:

The output variable will be active during any hour in which the schedule value is >0

If you want to report only one schedule named MiscElecLoad_1 you should do it like so:

Output:Variable,
    MiscElecLoad_1,          !- Key Value
    Schedule Value,          !- Variable Name
    Timestep;                !- Reporting Frequency

Edit:

I loaded your 1minschedule csv 1minSchedule.csv file using pandas, Python (with pandas), and I filtered it to find the timestamps where you have a 0 value, meaning the Output:Variable Output:Variable doesn't report. It happens for only 6 values, all of which are around 23:30:

2005-06-12 23:32:00    0.0
2005-06-12 23:33:00    0.0
2005-06-12 23:34:00    0.0
2005-06-12 23:35:00    0.0
2005-06-12 23:36:00    0.0
2005-06-12 23:37:00    0.0

So that explains your problem between 23 and 24.

(It would have been helpful to see a graph showing the discrepancy).

Anyways, from a cursory look I'd say your Output:Variable is wrong. Here's what you have:

Output:Variable,
    *,                       !- Key Value
    Schedule Value,          !- Variable Name
    Timestep,                !- Reporting Frequency
    MiscElecLoad_1;          !- Schedule Name

I suspect you don't understand what Schedule Name actually does. See the I/O Reference Guide, but in short:

The output variable will be active during any hour in which the schedule value is >0

If you want to report only one schedule named MiscElecLoad_1 you should do it like so:

Output:Variable,
    MiscElecLoad_1,          !- Key Value
    Schedule Value,          !- Variable Name
    Timestep;                !- Reporting Frequency

Edit:

I loaded your 1minSchedule.csv file using Python (with pandas), and I filtered it to find the timestamps where you have a 0 value, meaning the Output:Variable doesn't report. It happens for only 6 values, all of which are around 23:30:

2005-06-12 23:32:00    0.0
2005-06-12 23:33:00    0.0
2005-06-12 23:34:00    0.0
2005-06-12 23:35:00    0.0
2005-06-12 23:36:00    0.0
2005-06-12 23:37:00    0.0

So that explains your problem between 23 and 24.

  SimulationControl,
    Yes,                     !- Do Zone Sizing Calculation
    No,                      !- Do System Sizing Calculation
    Yes,                     !- Do Plant Sizing Calculation
    No,                      !- Run Simulation for Sizing Periods
    Yes;                     !- Run Simulation for Weather File Run Periods

(It would have been helpful to see a graph showing the discrepancy).

Anyways, from a cursory look I'd say your Output:Variable is wrong. Here's what you have:

Output:Variable,
    *,                       !- Key Value
    Schedule Value,          !- Variable Name
    Timestep,                !- Reporting Frequency
    MiscElecLoad_1;          !- Schedule Name

I suspect you don't understand what Schedule Name actually does. See the I/O Reference Guide, but in short:

The output variable will be active during any hour in which the schedule value is >0

If you want to report only one schedule named MiscElecLoad_1 you should do it like so:

Output:Variable,
    MiscElecLoad_1,          !- Key Value
    Schedule Value,          !- Variable Name
    Timestep;                !- Reporting Frequency

Edit:

I loaded your 1minSchedule.csv file using Python (with pandas), and I filtered it to find the timestamps where you have a 0 value, meaning the Output:Variable doesn't report. It happens for only 6 values, all of which are around 23:30:

2005-06-12 23:32:00    0.0
2005-06-12 23:33:00    0.0
2005-06-12 23:34:00    0.0
2005-06-12 23:35:00    0.0
2005-06-12 23:36:00    0.0
2005-06-12 23:37:00    0.0

So that explains your problem between 23 and 24.

Edit 2:

In the output you show, you never include the timestamp, but your SimulationCOntrolSimulationControl has Run Simulation for Sizing Periods:

  SimulationControl,
    Yes,                     !- Do Zone Sizing Calculation
    No,                      !- Do System Sizing Calculation
    Yes,                     !- Do Plant Sizing Calculation
    No,                      !- Run Simulation for Sizing Periods
    Yes;                     !- Run Simulation for Weather File Run Periods

This means that your eplusout.csv will include, at the top, data for your sizing periods. This could cause an offset when you are comparing stuff.

I did test do dummy example hourly schedule that I added to the example file 1ZoneUncontrolled.idf and I got this misalignment schedule initially (actually I found it because the output length was not 8760 but 8808 since I had two design days in my file (8670 + 2*24hrs = 8808).

After realigning the data (or just not run it for Sizing Periods), the input matches the output perfectly.