developer (c43b1)

CHARMM Developer Guide

This document provides a basic guide for understanding CHARMM's
architecture, implementation, and development protocols and tools.
Prospective developers are urged to familiarize themselves with
its contents.


* Implement | CHARMM Implementation and Management
* Directories | What directories are used to store what information
* Standards | Standards (rules) for writing CHARMM code
* Tools | Tools for CHARMM developers
* Modify | The procedure for modifying anything in CHARMM
* Document | How to document CHARMM commands and features
* API | How to generate low-level documentation from code
* Checkin | How to deposit your development version into the
central library


Top
CHARMM Implementation and Management

CHARMM is implemented as a single program package, which is
developed for use on a variety of platforms. The single source
structure makes the program easier to handle and promotes the
program's integrity.

CHARMM was originally written in FLECS, FORTRAN77 and C languages.
Before FORTRAN77, FLECS allowed us to use a variety of
control constructs, e.g., WHEN-ELSE, WHILE, UNLESS, etc. A FLECS to
FORTRAN translator was used to process FLECS source code to produce
FORTRAN source. With CHARMM 23, the FLECS source code was converted
to FORTRAN 77. CHARMM 23f2 and later versions are fully in FORTRAN,
except for some machine-specific codes written in C. All new
code should be written in FORTRAN 95.

Since CHARMM version 22, all files are maintained by utilizing
software engineering tools. The Subversion utility is used to maintain
the CHARMM source code, documentation and other supporting files.
The Subversion repository resides on charmm.hanyang.ac.kr. The CHARMM
manager controls both the developmental and released versions of the code.
He schedules contributions from all CHARMM developers.


Top
CHARMM Directory Structure


are used throughout the document. ~/ is the parent directory that
contains the CHARMM main directory, ~/cnnXm. nn is the version
number, X is the version trunk designator (a for alpha or
developmental, b for beta release and c for gamma or general release)
and m is the revision number. For example, c24b1 is CHARMM version 24
beta release revision 1.

Directory Purpose
------------------ ---------------------------------------------------
~/cnnXm The main directory of the current CHARMM version.
The install.com installation script runs in this directory.

~/cnnXm/source Source files.

~/cnnXm/doc Documentation

~/cnnXm/test Testcases

~/cnnXm/toppar Standard topology and parameter files.

~/cnnXm/support Holds various support programs and data files for
CHARMM. » support

~/cnnXm/tool Contains other CHARMM processing/management tools.

~/cnnXm/build Contains Makefile, module makefiles and the log
file of the install make command for each machine
in the subdirectory named after the machine type.

~/cnnXm/lib Contains library files

~/cnnXm/exec Will hold executables


Top
Standards (rules) for writing CHARMM code


Because CHARMM is developed by various groups, there are a number of
standards to which all contributors must adhere in order for the
program to remain modifiable, usable, and transferable. The rules
which have been established towards this end are listed below.

1) CHARMM module and subroutine structure:

Fortran modules should be used for all code when possible. The
general form of a CHARMM fortran module is:

module SAMPLEMOD
! Comments describing the general function of the module
use chm_kinds
implicit none

! Declarations of public variables
! Declarations of private variables

contains

subroutine SUBROUTINE1(arg1,arg2,...)
.
end subroutine SUBROUTINE1

subroutine SUBROUTINE2(arg1,arg2,...)
.
end subroutine SUBROUTINE2
.
.

!----- other subroutines and functions --------------!

end module SAMPLEMOD

The subroutines in a CHARMM module might include, for example,
setup subroutines, memory allocation/deallocation subroutines,
output subroutines, and the principal subroutines for the
method.

A subroutine in CHARMM should have the following general form:

subroutine DOTHIS(arg1,arg2,....
! A comment which describes the purpose of this subroutine.
! This may include important variables and what their use is
! to aid in understanding and modifying the routine.
! A description of all passed arrays and arguments if
! users need to call this routine.

use chm_kinds
use dimens (if dimensioned common blocks are included)
use number (if commonly used real numbers are used)
use somemodule, only: var1, var2, func1, sub1

implicit none

!---- declare all passed variables here --------
real(chm_real), intent(in) :: arg1
integer(chm_int), intent(out) :: arg2

!---- local ------------
Declarations of ALL local variables and parameters.
.
data statements at end of declarations.

!----- begin -----------
.
Code (liberally documented through comments)
.
end subroutine DOTHIS

Note that data statements, if present, come after all declarations
and parameter statements, but before the first line of executable code.

The use of subroutines outside of modules should be avoided because
the compiler does not check their arguments.

2) All code should be written clearly. Since the code must be
largely self-documenting, clarity should not be sacrificed for
insignificant gains in efficiency. Variable, function, subroutine
and module names should be chosen with care so as to help illustrate
their purpose. Avoid using single letter variable names except
for scratch variables in simple loop constructs. Comments should be
used where the function of the code is not obvious. Define/explain
important variables. Use the appropriate "intent" attribute (in, out,
inout) in variable declarations wherever possible.

3) Input/Output
a) The RDCMND routine should be used to read lines from the
command stream. XTRANE should be called to be sure that the
entire command line is parsed.
b) Short outputs, messages, warnings, and error should be sent to
unit OUTU (accessed by USE stream) for output. All output should
posess print level protection, e.g., if(prnlev>2) write(outu...
c) Any warning and error message should state which subroutine
generated it.
d) PSF and parameter unformatted I/O file formats must remain
upward compatible. Use an ICNTRL array element to indicate
which version of CHARMM wrote the file. Such upward
compatibility must be maintained only across release
versions of CHARMM. In other words, a file format for the
developmental version may be freely changed until a new release
version is generated, at which point all future versions must
be able to read it.
e) Use as many significant digits as needed but not more.
Do not use list directed output (use of "*" for format) or print.
In particular,
write(outu,*) var1, var2
print *, "Value is", e_variable
should not be used. It makes output unreadable and makes testing on
different machines difficult.
g) All output must be performed based on the PRNLEV value. This
is used, for example, to restrict I/O to node_0 in parallel
implementations of the code. For example,

write (OUTU,'(FORMAT)') ITEMs

should be coded as

if (PRNLEV.GT.2) write (OUTU,'(FORMAT)') ITEMs

where N is an appropriate print level (always >= 2; see also
miscom.doc).

4) All error conditions must terminate with a CALL WRNDIE(...) statement;
direct calls to DIE should not be used. The first argument is the
severity of the error, the second argument must contain the source
file in angle brackets, and the routine name of the location of
the error condition. The third argument contains a string
describing the error condition.

call WRNDIE(-3,'<tamd.src> tamd_allocate', &
'Failed to allocate memory for islct array')

5)
A. Use subroutines chmalloc and chmdealloc from module memory
to allocate and deallocate memory.

Example:

module mymod

use chm_kinds
integer, allocatable, dimension(:) :: myints
real(chm_real), allocatable, dimension(:) :: myreals

contains

subroutine mystart(natom)
use memory
integer, intent(in) :: natom
call chmalloc('mymod.src', 'mystart', 'myints', natom, intg=myints)
call chmalloc('mymod.src', 'mystart', 'myreals', natom, crl=myreals)
end subroutine mystart

subroutine myfinish(natom)
use memory
integer, intent(in) :: natom
call chmdealloc('mymod.src', 'myfinish', 'myreals', natom, crl=myreals)
call chmdealloc('mymod.src', 'myfinish', 'myints', natom, intg=myints)
end subroutine myfinish

end module mymod

B. If possible, combine memory allocation statements in a
separate subroutine. Do the same for memory deallocation.

6) Arrays should be dimensioned with a constant or integer variable
where possible. Do not use (*) when dimensioning arrays passed as
arguments; be sure to pass the dimensioning information
also. Arrays cannot change shape or type when passed.

subroutine NEWFORCE(natom,force,fsum)
use chm_kinds
implicit none
integer(chm_int),intent(in) :: natom
real(chm_real),intent(out) :: fsum
real(chm_real),intent(inout),dimension(3,natom) :: force
---or---
real(chm_real),intent(inout) :: force(3,natom)

Check for array overflows.

7) Error checking in general should be as complete as possible.
Consider checking for overflows (reciprocals of very small
numbers, exponentials of very large numbers, etc.), square roots
of negative numbers, arccosine or arcsine of numbers of absolute
value greater than one, etc. Code should contain checks for error
conditions where it will not impact performance. Use compiler
flags for checking, then remove checking flags for production
compiling and code submission.

7) The code should not use non-standard Fortran 95 features.
Such features must be restricted to the machine dependent modules,
or encapsulated in "##IF - ##ELSE - ##ENDIF" preprocessor or
equivalent CPP #if KEY_THISKEY==1 - #else - #endif constructs.

8) Do not use obsolescent or deprecated Fortran constructs, only use
what is in the current standard.
Do not create common blocks, and use the established common blocks
only when necessary.
Do not use entry points.
Do not use computed or assigned goto statements.
Avoid "goto" when other constructs are available such as "if," "case,"
"cycle," and "exit."

9) Functions should never be called with a "call" statement.

10) The generic form of an intrinsic function should be used whenever
possible. For example, use SQRT(DP) rather than DSQRT(DP).

11) Real or integer constants should be defined as parameters.
real(chm_real),parameter :: ONE=1.0D0, THREE=3.0D0, FIVE=5.0D0, &
SEVEN=7.0D0
integer(chm_int),parameter :: MAXATM=99999

See ltm/number_ltm.src for frequently used numbers.
Real numbers may never be placed in a calling sequence.
All physical constants should be declared as parameters in
ltm/consta_ltm.src
Constants and numbers can be used by adding

use consta

to routines or modules.

12) Routines should have no implicitly declared variables. This means that
all variables and arrays, whether passed or not, must be explicitly
declared. Each module must thus contain

implicit none

as the first statement after any "use" statements and before any
declarations. This obviates the need for having the implicit none
statement in each of the subroutines contained in the module.
A routine that is not contained in a module must have the
implicit none statement as the first statement after any "use"
statements and before any declarations.

13) There is no upper or lower case rule in CHARMM except that any
variable or subroutine name should have consistent case throughout
all of CHARMM code. It is helpful to use all caps for parameter
variables.

14) No tabs should appear in code or documentation.

15) All strings must be stored in character variables. Use
character(len=<n>) for character declarations, where <n> is the
length of the string. a "*" may be used for the length of a passed
string but this is discouraged.

16) For routine command parsing, the keyword parsing functions INDXA,
GTRMA, GTRMF, GTRMI, and NEXTA4 should be used.

17) The recommended length for names of frequently used variables is
4-10 characters. Avoid single letter variables, except as indices
for simple loops. Avoid overriding standard Fortan words such as
SUM or TYPE.

18) All variables must be declared with a kind. Use the kinds available
in chm_kinds_ltm.src, the CHARMM variable kinds (chm_kinds) module. If a
new kind is used, add it to the chm_kinds module.

19) All variables must be initialized before first use. Most
initialization is done in the setup or initialization routine in a
module.

20) Other coding conventions make it easier to search through text for
particular strings using the SEARCH, fpat, or grep commands.
Poorly placed spaces can make it very difficult to maintain code.
There cannot be a space within a variable name. Here are some
other examples;

Good Please Avoid
----------------- ------------------
GOTO GO TO
CALL DOSOME(... CALL DOSOME(...
CALL DOSOME (...
ARRAY(5) = 20
ARRAY(5)=20 ARRAY (5) = 20

21) The ltm directory contains modules that have no dependencies on
other modules, except for the chm_kinds module. Examples are modules
containing global parameters and variables.

22) Avoid duplicating code. If a defect is found in some code, and there
are multiple copies of it, the remedy must be applied to all copies.
If code is not duplicated, all its users benefit from any improvement
to it.


Top
CHARMM Developer Tools

strongly support multiplatform development efforts. CHARMM tools are
utility programs/procedures for installation, modification,
optimization, etc. The utility procedures
for makefile generation are located in ~/cnnXm/tool.
The preprocessor PREFX and the FLECS to FORTRAN translator FLEXFORT
are no longer needed since CHARMM
c43b1 and c23f2 respectively.
They are no longer maintained starting from these and later distribution versions.


* (prefx/">prefx.doc)">(prefx | CHARMM Source Code Preprocessor
* makemod | Module Makefiles and Optimization Procedure


Top
Module Makefiles and Optimization

The installation script install.com works with a set of makefiles in
~/cnnXm/build/{machine_type}. These makefiles play the key role in
developing, optimizing and porting CHARMM code on the machine you are
working with.


[1] Porting to Other Machines

You may begin with the given set of makefiles for a machine close
in the architecture to the one to which you intend to port CHARMM.
First you have to decide a name for the machine platform. For
example, IBMRS was chosen for the IBM RS/6000 series.

cp -r ~/cnnXm/build/{closely_related_machine_type} \
~/cnnXm/build/{your_chosen_machine_type}

Then delete Makefile in the new build directory and remane
Makefile_{closely_related_machine_type} to Makefile_{your_machine_type}.
You may have to modify compile commands and compiler flags in the
Makefile template.
Study carefully ~/cnnXm/install.com and modify it if necessary.
In most cases, you just need to correct echo messages to address your
machine properly. Then issue the install.com command.


[2] Optimization

Once the makefiles are working properly, you can carry out a
compiler level optimization for the CHARMM version. FORTRAN compile
macro's are defined in Makefile_{machine_type}, e.g., $(FC1), $(FC2),
$(FC3), etc. Compiler options are bound to these compile macros. You
may inspect each module makefiles and set a proper compile command for
a given FORTRAN source. For example, the following are the default
optimization flags for the c24b1 release. Most of source files are
compiled by $(FC2) execpt

build/convex/energy.mk
$(FC0) ehbond.f
$(FCR) enefst2.f
$(FCR) enefst2q.f
$(FC3) enefvect.f

build/convex/image.mk
$(FCR) imnbf2p.f
$(FC3) imnbfp.f
$(FC0) nbondm.f

build/convex/manip.mk
$(FC0) corman.f
$(FC3) fshake.f
$(FCR) fshake2.f

build/convex/nbonds.mk
$(FCR) enbf2.f
$(FCR) enbf3.f
$(FCR) enbf4.f
$(FCR) enbf5.f
$(FC3) ewaldf.f
$(FCR) ewaldf2.f
$(FCR) nbndf2p.f
$(FC3) nbndfp.f

build/convex/quantum.mk
$(FC0) qmdata.f
$(FC0) qmene.f
$(FC0) qmjunc.f
$(FC0) qmpac.f
$(FC0) qmset.f


[3] Generating Module Makefiles

We have included scripts that find all module dependencies. When you
want to create the full set of module makefiles, you may use setmk.com
in ~/cnnXm/tool.

setmk.com UNX

This generates makefiles in ~/cnnXm/build/UNX, which install.com
copies to ~/cnnXm/build/{machine-type} as needed.


[4] Usage Note on makemod

When you generate module.mk files from scratch, the FORTRAN
compile macro $(FC2) is used for all source files. In order to set
the compiler option for further optimization, you have to modify
the module makefiles to set the macro manually.


Top
The procedure for modifying anything in CHARMM

This procedure describes the steps which should be taken when
modifying a source file in CHARMM. When you are developing CHARMM
source code, always maintain close contact with the CHARMM manager
and other developers. Inform them your development plan and which
files you are working on. Checkin:: for the procedures
to follow when submitting your developmental code to the CHARMM manager.

1) Get a copy of the current development code. If you are a CHARMM
developer and plan to integrate your program into CHARMM in the
future, make sure that you obtain the most current revision from
Subversion. Check with the CHARMM manager.

2) Once you obtain the code, you are branching out from the main
CHARMM source code control system. You should record details
of modification so that you may reproduce them when you check your
files in with the CHARMM manager.

3) While you make modifications and debug them, follow the guidelines
in *note Standards::, so that CHARMM code will be consistent.
If your modification does not involve any changes in the source file
directory structure and makes no changes in USE statements,
you may use the module makefiles supplied (with the extension .mk)
in ~/cnnXm/build/UNX. If you add/remove any source files,
reorganize them, modify any USE statements or are porting to
a machine that is not already supported, you have to build the
relevant module make files. makemod:: for more
information on makemod.

4) In your local ~/cnnXm directory, you may issue the install.com
command to build the library and the executable.
» install Install.
Your library is built in ~/cnnXm/lib/{machine_type} and the
executable will be in ~/cnnXm/exec/{machine_type}. You may find
the log file {machine_type}.log in ~/cnnXm/build/{machine_type}.

5) If your modification involves a new feature, you should either
modify an existing test case or make a new test case to demonstrate
and check its operation. » testcase for a
description of the tests currently available. If you add a new test
case, update the ~charmm/doc/testcase.doc file. Each new test case
should run in 1 second or less on a modern workstation.

6) If your change involves adding or modifying a command or adding or
modifying a feature, modify the existing documentation or if none is
available, create new documentation. Make sure that the emacs info
program can read the document and the format of your documentation
is consistent with other documents. Document::.


Top
How to Document CHARMM Commands and Features

Documentation is an integral part of CHARMM developments. In order to
document commands and features under development in a consistent
manner, the following documentation format is recommended. All
documentation should be accessible (readable) through the emacs info
facility. If you do not know how to insert the info directives, ask the
introduced, a new .doc file should be created. For modifications or
extensions of existing CHARMM modules/functions, the preexisting .doc
file should be revised.

Each documentation file, with the extension .doc, should contain

1) One brief paragraph describing the motivation, theory, or
procedure relevant to the feature being documented. Here,
a few references can be given.

2) A table of contents of the documentation (to serve as the info
menu).

3) The command syntax.

4) A complete description of all the commands, sub-commands, and
command options. The syntax, defaults and file names involved
should be described. A brief description of what the command
accomplishes should also be given. The order in which various
commands should be invoked should be described. Relevant commands
and subcommands can be cross-referenced with a key.

5) One or two examples involving the concepts and commands described
(No output listing).

The same notation should be followed throughout the documentation.

[...] optional, can be present only once, if at all.

{...} can be repeated any number of times, must be present
at least once.

[{...}] or [{...}] can either be missing or be present any
number of times.

n{...} must be present exactly n times.

<A|b> either A or B must be present.

Syntax definitions will use literal keywords such as VIBRan,
READ, MINI, VERLet, etc. These are to be typed as such.

Syntax definitions can also use dummy keywords such as atom_name,
atom_index and atom_type. The meaning and variable type can be listed
just after the syntax notation.

For literal keywords the documentation and examples will use
uppercase characters immediately followed by zero or more lower case
characters. Dummy keywords will be written in all lower case.


Top
API Documentation

As a complement to the required command and feature documentation,
the free Doxygen tool (http://www.doxygen.org/) can automatically
generate low-level documentation from the source code. Doxygen reads
declarations of modules, subroutines, and variables, and generates HTML
with cross-references showing the relationships between them.

Doxygen also recognizes Fortran comments beginning with !> as text to
include in the HTML output. Some examples of such comments are in
source/pert/lambdadyn.src.

Before you run Doxygen on CHARMM code, download the Doxygen 1.6
source distribution and apply tool/doxygen.patch as follows:

cd doxygen-1.6
patch -p0 < ../charmm/tool/doxygen.patch

and follow the Doxygen installation instructions. Then the shell command

cd ../charmm
doxygen tool/Doxyfile

generates documentation in a directory named apidoc. A good starting
point for browsing is apidoc/html/files.html.

If you have Graphviz (http://www.graphviz.org/) installed, Doxygen
can generate call diagrams for each subroutine. To do this, edit
tool/Doxyfile and change CALL_GRAPH and CALLER_GRAPH to YES.


Top
Checkin Procedure in CHARMM Management System

The following rules have been established to minimize conflicts
and delays and to allow for error-free integration of CHARMM
developments from many scientists.

1) It is always wise to inform the CHARMM manager about your
development plan and timetable so that he may better arrange the
administrative schedule and also prevent you from duplicating the work
of others. The list of files you are working on and the nature of
the modifications should be reported in advance.

2) Developments must be submitted to the CHARMM manager by
December 30 for inclusion in the February distributions or
June 30 for the August distributions.

3) Be certain that the submitted developments are based on the most
recent development version of CHARMM. The check-in package
(see below) should compile out-of-the-box when merged with the
base version.

4) Prior to check-in, run "test.com" after integration of the
check-in package with the appropriate base version of CHARMM.
Compare the results in the output directory with those obtained
when using the base version. If you are introducing new
preprocessor (pref.dat) keywords to control the compilation of
code for new features (which is recommended), check the test.com
results for executables produced both with and without the new
keyword(s).

5) The check-in or submission package should include the following:
* modified source files (using the CHARMM source directory structure),
* updated or new documentation » * files, and
* updated testcase files

These files should be assembled in a tar archive conforming to the
CHARMM distribution directory structure.

6) Post a completed project form (http://charmm.hanyang.ac.kr/172) to
the CHARMM development bulletin board (http://charmm.hanyang.ac.kr/).
The project form should contain a succinct description of the
submitted modifications and new features, the name(s) and institutional
affiliations of the developer(s), the date, the base CHARMM version,
new preprocessor keywords, and lists of the new and modified files.
Upload your tar archive as an attachment to the project form.