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started on stretched-grid instructions
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@LiamBindle
LiamBindle committed Oct 17, 2020
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329 changes: 329 additions & 0 deletions docs/source/_static/sg-interactive.html
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<head>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Load plotly.js into the DOM -->
<script src='https://cdnjs.cloudflare.com/ajax/libs/mathjs/7.1.0/math.min.js'></script>
<script src='https://cdn.plot.ly/plotly-latest.min.js'></script>

<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
<link href="https://cdnjs.cloudflare.com/ajax/libs/noUiSlider/14.6.1/nouislider.min.css" rel="stylesheet">
<style>
.container {
display: flex;
flex-direction: column;
height: 100%;
width: 95%;
max-width: 980px;
align-items: center;
justify-content: center;
margin-left: 0.5em;
}


.sg-figure {
order: 1;
flex-grow: 1;
width: 100%;
max-width: 980px;
height: 100%;
justify-content: center;
overflow: hidden;
padding: 0;
margin: 0;
}

.parameter-slider {
order: 2;
width: 100%;
max-width: 980px;
border: 1px #ccc solid;
padding: 1em;
margin: 0.2em;
}

input {
padding-left: 0.5em;
}

.slider-wrapper {
margin-top: 0.5em;
}

.slider-wrapper .noUi-connect {
background: #636363;
}
</style>
<script src="https://cdnjs.cloudflare.com/ajax/libs/noUiSlider/14.6.1/nouislider.min.js"></script>

</head>
<body>
<div class="container">
<div class="sg-figure">
<div id='myDiv'></div>
</div>
<div class="parameter-slider">
<label for="SF">Stretch factor: </label>
<input type="number" id="SF" value="3.0" name="SF" min="1.0" max="15.0" oninput="update_plot()">
<div class="slider-wrapper">
<div id="SF-slider"></div>
</div>
</div>
<div class="parameter-slider">
<label for="TX">Target longitude: </label>
<input type="number" id="TX" value="273.00" name="TX" min="0.0" max="360.0" oninput="update_plot()">
<div class="slider-wrapper">
<div id="TX-slider"></div>
</div>
</div>
<div class="parameter-slider">
<label for="TY">Target latitude: </label>
<input type="number" id="TY" value="37.50" name="TY" min="-90.0" max="90.0" oninput="update_plot()">
<div class="slider-wrapper">
<div id="TY-slider"></div>
</div>
</div>
</div>
<script>
function unpack(rows, key) {
return rows.map(function (row) { return row[key]; });
}

function rotate_vector(v, k, theta) {
var t1 = math.multiply(v, math.cos(theta));
var t2 = math.multiply(math.cross(k, v), math.sin(theta));
var t3 = math.multiply(k, math.dot(k, v) * (1.0-math.cos(theta)));
return math.add(t1, t2, t3)._data;
}

function cartesian_to_spherical(v) {
var y_sph = math.asin(v[2]);
var x_sph = math.atan2(v[1], v[0]);
return [x_sph, y_sph];
}

function spherical_to_cartesian(v) {
var x_car = math.cos(v[1]) * math.cos(v[0]);
var y_car = math.cos(v[1]) * math.sin(v[0]);
var z_car = math.sin(v[1]);
return [x_car, y_car, z_car];

}

function deg2rad(v) {
for(var i = 0; i < v.length; ++i) {
v[i] = v[i] * math.pi/180;
}
return v;
}

function rad2deg(v) {
for(var i = 0; i < v.length; ++i) {
v[i] = v[i] * 180/math.pi;
}
return v;
}

function schmidt_transform(v, s) {
var D = (1 - s*s) / (1 + s*s);
v[1] = math.asin((D + math.sin(v[1])) / (1 + D * math.sin(v[1])));
return v;
}

function sg_transform(x, y, s, tx, ty) {
// Convert xy to radians
x = x * math.pi / 180;
y = y * math.pi / 180;
tx = tx * math.pi / 180;
ty = ty * math.pi / 180;
// Calculate rotation about x, and z axes
x0 = math.pi;
y0 = -math.pi/2;
theta_x = ty - y0;
theta_z = tx - x0;
// Apply schmidt transform
var v = schmidt_transform([x, y], s);
// Convert to cartesian coordinates
v = spherical_to_cartesian(v);
// Rotate about y axis
yaxis = math.matrix([0, 1, 0]);
v = rotate_vector(math.matrix(v), yaxis, theta_x);
// Rotate about z axis
zaxis = math.matrix([0, 0, 1]);
v = rotate_vector(math.matrix(v), zaxis, theta_z);
// Convert back to spherical coordinates
v = cartesian_to_spherical(v);
// Convert back to degrees and return
x = v[0] * 180 / math.pi;
y = v[1] * 180 / math.pi;
return [x, y];
}


function create_sg_data(sf, tx, ty) {
var data = [];

var cs_table = [
[-55.0, -48.53540802286467, -41.59979318868607, -34.20342833932976, -26.398120477217244, -18.28298505985221, -9.999999999999988, -1.7170149401478112, 6.398120477217223, 14.203428339329768, 21.599793188686025, 28.53540802286464, 35.000000000000014],
[-35.26438968275467, -38.03334585043359, -40.421993720970114, -42.36780515862268, -43.81067497331048, -44.69959875364784, -44.99999999999999, -44.69959875364784, -43.81067497331048, -42.36780515862268, -40.421993720970114, -38.03334585043359, -35.26438968275467],
[-55.0, -48.53540802286467, -41.59979318868607, -34.20342833932976, -26.398120477217244, -18.28298505985221, -9.999999999999988, -1.7170149401478112, 6.398120477217223, 14.203428339329768, 21.599793188686025, 28.53540802286464, 35.000000000000014],
[35.26438968275467, 38.03334585043359, 40.421993720970114, 42.36780515862268, 43.81067497331048, 44.69959875364784, 44.99999999999999, 44.69959875364784, 43.81067497331048, 42.36780515862268, 40.421993720970114, 38.03334585043359, 35.26438968275467],
[-55.0, -55.0, -55.0, -55.0, -55.0, -55.0, -55.0, -55.0, -55.0, -55.0, -55.0, -55.0, -55.0],
[-35.26438968275467, -29.38699140229555, -23.509593121836446, -17.632194841377334, -11.754796560918223, -5.877398280459113, 0.0, 5.877398280459113, 11.754796560918223, 17.63219484137734, 23.509593121836446, 29.38699140229555, 35.26438968275467],
[35.000000000000014, 35.0, 35.0, 35.0, 35.000000000000014, 35.000000000000014, 35.000000000000014, 35.000000000000014, 35.000000000000014, 35.0, 35.0, 35.0, 35.000000000000014],
[-35.26438968275467, -29.38699140229555, -23.509593121836446, -17.632194841377338, -11.754796560918223, -5.877398280459113, 0.0, 5.877398280459113, 11.754796560918223, 17.632194841377338, 23.509593121836446, 29.38699140229555, 35.26438968275467],
[35.00000000000003, 41.46459197713539, 48.40020681131399, 55.796571660670246, 63.60187952278279, 71.71701494014782, 80.00000000000001, 88.28298505985221, 96.39812047721722, 104.20342833932976, 111.59979318868602, 118.53540802286464, 125.00000000000001],
[-35.26438968275467, -38.03334585043359, -40.421993720970114, -42.36780515862268, -43.81067497331048, -44.69959875364784, -44.99999999999999, -44.69959875364784, -43.81067497331048, -42.36780515862269, -40.421993720970114, -38.03334585043359, -35.26438968275467],
[35.00000000000003, 41.46459197713539, 48.40020681131399, 55.796571660670246, 63.60187952278279, 71.71701494014782, 80.00000000000001, 88.28298505985221, 96.39812047721722, 104.20342833932976, 111.59979318868602, 118.53540802286464, 125.00000000000001],
[35.26438968275467, 38.03334585043359, 40.421993720970114, 42.36780515862268, 43.81067497331048, 44.69959875364784, 44.99999999999999, 44.69959875364784, 43.81067497331048, 42.36780515862269, 40.421993720970114, 38.03334585043359, 35.26438968275467],
[125.00000000000001, 125.00000000000001, 125.00000000000001, 125.00000000000001, 125.00000000000001, 125.00000000000001, 125.00000000000001, 125.00000000000001, 125.00000000000001, 125.00000000000001, 125.00000000000001, 125.00000000000001, 125.00000000000001],
[-35.26438968275467, -29.38699140229555, -23.509593121836446, -17.632194841377338, -11.754796560918223, -5.877398280459113, 0.0, 5.877398280459113, 11.754796560918223, 17.632194841377338, 23.509593121836446, 29.38699140229555, 35.26438968275467],
[125.00000000000001, 131.46459197713534, 138.400206811314, 145.79657166067025, 153.60187952278275, 161.71701494014783, 170.0, 178.28298505985217, 186.39812047721728, 194.20342833932978, 201.59979318868605, 208.53540802286466, 215.0],
[35.264389682754654, 38.0333458504336, 40.421993720970114, 42.36780515862268, 43.81067497331049, 44.69959875364784, 45.00000000000001, 44.69959875364784, 43.81067497331049, 42.36780515862268, 40.421993720970114, 38.0333458504336, 35.264389682754654],
[125.00000000000001, 131.46459197713534, 138.400206811314, 145.79657166067025, 153.60187952278275, 161.71701494014783, 170.0, 178.28298505985217, 186.3981204772172, 194.20342833932975, 201.59979318868602, 208.5354080228646, 214.99999999999997],
[-35.26438968275464, -38.03334585043357, -40.421993720970086, -42.367805158622645, -43.81067497331046, -44.699598753647805, -44.999999999999986, -44.699598753647805, -43.81067497331046, -42.367805158622645, -40.421993720970086, -38.03334585043357, -35.26438968275464],
[-145.00000000000003, -138.5354080228647, -131.59979318868602, -124.20342833932976, -116.39812047721726, -108.28298505985221, -100.0, -91.7170149401478, -83.60187952278277, -75.79657166067024, -68.40020681131399, -61.46459197713532, -55.0],
[35.26438968275464, 38.03334585043359, 40.4219937209701, 42.36780515862265, 43.81067497331048, 44.69959875364784, 44.99999999999999, 44.69959875364784, 43.81067497331048, 42.36780515862265, 40.4219937209701, 38.03334585043359, 35.26438968275464],
[-145.00000000000003, -138.5354080228647, -131.59979318868602, -124.20342833932982, -116.39812047721726, -108.28298505985221, -100.0, -91.7170149401478, -83.60187952278277, -75.79657166067024, -68.40020681131399, -61.46459197713532, -55.0],
[-35.26438968275464, -38.03334585043358, -40.4219937209701, -42.36780515862265, -43.81067497331048, -44.69959875364784, -44.99999999999999, -44.69959875364784, -43.81067497331048, -42.36780515862265, -40.4219937209701, -38.03334585043359, -35.264389682754654],
[-145.00000000000003, -145.0, -145.00000000000003, -145.00000000000003, -145.00000000000003, -145.00000000000003, -145.0, -145.00000000000003, -145.0, -145.00000000000003, -145.00000000000003, -145.0, -145.00000000000003],
[35.26438968275464, 29.386991402295543, 23.509593121836435, 17.632194841377334, 11.754796560918209, 5.877398280459112, 0.0, -5.877398280459103, -11.7547965609182, -17.63219484137732, -23.509593121836417, -29.386991402295532, -35.26438968275464],
]

for (var i = 0; i < 12; i++) {
x = cs_table[2 * i];
y = cs_table[2 * i + 1];
var x2 = [];
var y2 = [];

for(var j = 0; j < x.length; j++) {

var t = [x[j], y[j]]
t = deg2rad(t)
t = spherical_to_cartesian(t)
t = rotate_vector(t, math.matrix([0, 0, 1]), 30)
t = cartesian_to_spherical(t)
t = rad2deg(t)

var xy = sg_transform(t[0], t[1], sf, tx, ty);
x2.push(xy[0]);
y2.push(xy[1]);
}
console.log(x2)
data.push({
type: 'scattergeo',
lon: x2,
lat: y2,
mode: 'lines',
line: {
width: 3,
color: "#000000"
},
showlegend: false,
})
}
return data;
}

var myDiv = document.getElementById('myDiv');

var layout = {
geo: {
projection: {
type: 'orthographic',
rotation: {
lon: -60,
lat: 10
},
},
showocean: true,
oceancolor: '#f0f0f0',
showland: true,
landcolor: '#bdbdbd',
showlakes: true,
lakecolor: '#f0f0f0',
showcountries: true,
lonaxis: {
showgrid: true,
gridcolor: '#636363'
},
lataxis: {
showgrid: true,
gridcolor: '#636363'
}
},
autosize: true,
};

var SF = 3.0;
var TX= 273.0;
var TY= 37.5;

var config = {responsive: true, showLink: false};

var data = create_sg_data(SF, TX, TY);
Plotly.newPlot("myDiv", data, layout, config);

function update_plot() {
var data = create_sg_data(document.getElementById('SF').value, document.getElementById('TX').value, document.getElementById('TY').value);
Plotly.react("myDiv", data, layout, { showLink: false });
}

var SF_slider = document.getElementById('SF-slider');
var TX_slider = document.getElementById('TX-slider');
var TY_slider = document.getElementById('TY-slider');

noUiSlider.create(SF_slider, {
start: [SF],
connect: 'lower',
step: 0.1,
range: {
'min': 1.0,
'max': 15.0
}
});

noUiSlider.create(TX_slider, {
start: [TX],
connect: 'lower',
step: 0.1,
range: {
'min': 0,
'max': 360
}
});

noUiSlider.create(TY_slider, {
start: [TY],
connect: 'lower',
step: 0.1,
range: {
'min': -90.0,
'max': 90.0
}
});

SF_slider.noUiSlider.on('update', function (values, handle) {
SF = values[handle];
document.getElementById('SF').value = values[handle];
var data = create_sg_data(SF, TX, TY);
Plotly.react("myDiv", data, layout, config);
});

TX_slider.noUiSlider.on('update', function (values, handle) {
TX = values[handle];
document.getElementById('TX').value = values[handle];
var data = create_sg_data(SF, TX, TY);
Plotly.react("myDiv", data, layout, config);
});

TY_slider.noUiSlider.on('update', function (values, handle) {
TY = values[handle];
document.getElementById('TY').value = values[handle];
var data = create_sg_data(SF, TX, TY);
Plotly.react("myDiv", data, layout, config);
});


// setTimeout(update_plot, 5000);

</script>
</body>
2 changes: 1 addition & 1 deletion docs/source/index.rst
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Expand Up @@ -34,7 +34,7 @@ Modeling Group at Harvard University <http://acmg.seas.harvard.edu/index.html>`_
:caption: Step-by-step Guides

step-by-step/plotting-output.rst
step-by-step/stretched-grid.rst
stretched-grid.rst


.. toctree::
Expand Down
6 changes: 0 additions & 6 deletions docs/source/step-by-step/stretched-grid.rst
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34 changes: 34 additions & 0 deletions docs/source/stretched-grid.rst
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Stretched-grid simulations
==========================

There are two steps to running a stretched-grid simulation:

#. You need a restart file for your specific stretched-grid. The easiest way
to get this is by regridding an existing restart file with GCPy.
#. You need to update the appropriate parameters in :file:`runConfig.sh`.

Before setting up a stretched-grid simulation, you need to decide on an appropriate
stretched-grid for your application.

Choosing stretched-grid parameters
----------------------------------

.. raw:: html

<iframe src="_static/sg-interactive.html" height="900px" width="100%" frameBorder="0"></iframe>


Regridding an existing restart file
-----------------------------------

todo

Updating :file:`runConfig.sh`
-----------------------------

todo



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